Watkins swooped in just the second minute to head home the only goal of the game from George Williams' cross.
The Bantams thought they had equalised just before the half hour mark but the recalled Josh Morris' shot from deep inside the box following a Tony McMahon corner somehow deflected wide of the post.
With Morris and Mark Marshall impressing on the wings, Phil Parkinson's men were playing were plenty of attacking zip but they just couldn't find that vital breakthrough.
On his home debut, Jamie Proctor fired narrowly wide from distance on the hour after Barnsley 'keeper Adam Davies mis-placed clearance had seen the ball land at the striker's feet with the goal vacant.
Barnsley's scoring opportunities after the restart were restricted to those largely created on the counter-attack, although Rory McArdle was needed to make vital blocks in the box from Josh Brownhill and Sam Winnall.
Playing in central midfield alongside Christopher Routis, McMahon had one last chance for City in the final minute of normal time but his free-kick from outside the area dropped just wide of Davies' near post.
FT: Bradford City 0 Barnsley 1
90+3min: Brownhill's swerving free-kick from distance is held by Williams.
90+2min: SUB - Barnsley bring on Otis Khan for Isgrove.
90min: There will be three minutes of time added on at the end of the match.
90min: McMahon's free-kick from just outside the box drops narrowly wide of Davies' near post.
88min: Nathan Clarke has now joined City's attack.
87min: YELLOW CARD - McMahon is booked for a late sliding tackle on Scowen just inside Barnsley's half of the pitch. The resulting free-kick from the Tykes eventually drops into the path of Hourihane just outside the box but his first time shot is sliced comfortably wide.
85min: A half-cleared Hourihane free-kick into the box eventually drops into the path of Scowen following a loose touch from Knott. Scowen drives into the box but his shot is blocked by the diving frame of Nathan Clarke.
82min: SUB - Barnsley bring on Josh Scowen for Fletcher.
76min: Darby is back on the pitch and playing again despite the knock.
75min: As Barnsley break with pace on the counter-attack, Conor Hourihane's low cut-back is blocked by the out-stretched leg of James Meredith before McArdle produces another important tackle to prevent Winnall tapping in the loose ball from yards out. The counter-attack came with Darby off the pitch and limping after coming off worse with a 50-50 tackle with George Williams seconds earlier.
72min: Fletcher's low shot from the edge of the area is comfortably held by Williams.
71min: SUB - The Bantams bring on Billy Knott for Routis.
65min: McMahon's shot from outside the box is pushed away by Davies.
62min: Fletcher looks to race onto Winnall's headed flick on but McArdle gets a vital touch on the ball and Williams is able to smother the ball at the striker's feet.
61min: Fletcher tries to wrestle his way into clear shooting space deep inside City's penalty box but Darby does just enough to partially block the forward's eventual strike on goal and Williams can gather.
60min: City go agonisingly close to finding an equaliser! Adam Davies races clear out of his box to try and kick away a ball into Barnsley's hald but his clearance is sliced and it lands at the feet of Proctor roughly 45 yards from goal. With Davies well out of his goal, Proctor gets his shot away early before nearby Barnsley players can close him down but his effort bounces wide of the post.
59min: As City try to clear the resulting Barnsley corner, the ball breaks to Brownhill just outside the box and his fierce rising effort is superbly tipped over by a diving save from Williams.
58min: What a superb tackle from McArdle! With City pushed up, Winnall plays the ball through to Josh Brownhill to leave him with a clear run on goal. McArdle gets around just in time, however, to block the behind for a corner. Any goal for Barnsley there would have been extremely hard for City to take after dominating the opening exchanges of the second period.
55min: SUB - With Billy Clarke limping off, the Irishman is replaced by Steven Davies.
53min: McMahon's teasing delivery into the box from a wide free-kick narrowly misses everyone before Davies just crawls the effort away as it threaten to sneak in by his far post. Even if McMahon's effort had of gone in, however, the goal would have been disallowed due to the linesman's flag for offside.
51min: Fletcher runs from wide into the penalty box, leaving Darby in his wake. As McArdle comes across to apply some pressure, the striker fires for goal and his low drive from an angled crashes into the side-netting by Williams' near post.
49min: Morris' low pass into the box finds Proctor. The striker tries to move into a shooting position but the ball breaks free to Morris again and the midfielder fires in a fizzing cross-come-shot that flashes wide of Davies' far post.
48min: Morris' teasing free-kick delivery from wide narrowly misses Routis and Billy Clarke in the middle before going into the arms of Davies.
47min: Marshall plays into the box towards Billy Clarke and the Irish striker fires in a low cross-come-shot bounces a yard or so wide of Davies' far post.
46min: Barnsley restart the match.
HT SUB - The Bantams are bringing on Nathan Clarke for Burke, presumably due to an injury for the young defender.
HT: Bradford City 0 Barnsley 1
45+2min: Morris' flighted cross towards the far post finds Marshall unmarked but instead of going for goal, the winger tries to lay off to Proctor but the pass is under-hit and Barnsley can clear.
45+1min: Fletcher looks to have the run of the ball for a second but a great tackle from Reece Burke denies the young striker a free run into City's penalty box. Seconds later, Marshall whips over a teasing near post cross but Davies is able to grab hold of the ball ahead of a lurking Proctor.
45min: There will be two minutes of time added on at the end of the first half.
45min: YELLOW CARD - Winnall is booked for a late challenge on Morris just inside Barnsley's half over by the far touchline.
41min: Morris' corner delivery is headed out by Long while under pressure from McArdle. McMahon moves around the bouncing ball to get his right foot in position before firing in a looping half-volley from just outside the box that flies wide of Davies' far post.
37min: Watkins heads narrowly wide of Williams' near post following Isgrove's cross from the byline.
35min: Winnall works himself a yard of shooting space just outside the box before curling in a drive that flashes just wide of Williams' far post.
34min: Great counter-attacking play from Routis and Mark Marshall sees the latter with space to run deep inside Barnsley's penalty area. Marshall eventually tees the ball back to Routis but the Frenchman's drive from just inside the box is blocked.
29min: McArdle seems to jump a tad too early as he sends a free header comfortably over the bar from a dangerous Morris corner delivery.
28min: From the resulting Tony McMahon corner delivery, Rory McArdle and Christopher Routis keep the attack alive with headers before Morris latches onto the loose ball to fire for goal from deep inside the box. The shot looks goal-bound until it takes a slight deflection at the last minute, sending just past the post despite the best efforts of a nearby City player.
27min: Josh Morris' purposeful run and cross sees the ball flash across the six yard box and Long uncomfortably put the ball behind for a corner.
19min: SUB - Barnsley are forced to take off Mawson, presumably due to an injury, and replace him with fellow central defender Marc Roberts.
12min: Sam Winnall connects with James Bree's cross but his header is some distance away from goal.
11min: Proctor is involved once more, this time wrestling possession away from Kevin Long as the ball bounces deep inside the Barnsley box. Proctor goes for a shot on the turn but his effort has the pace taken out of it by the frame of Alfie Mawson and Davies can gather.
10min: Proctor is off again shortly afterwards, this time racing after a searching forward pass from James Meredith. Davies this time just beats Proctor to the ball but his momentum takes some of his body out of the box. The home fans cry foul but referee and linesman deem that Davies has just kept the ball inside the box while it was in his possession.
10min: Stephen Darby's ball in behind has Jamie Proctor interested as the striker races towards Barnsley's penalty box. With Davies out of his goal, Proctor gets a touch on the ball but he is unable to collect the pass fully and a grateful Barnsley shot-stopper is able to gather.
9min: The ball breaks free to Ashley Fletcher and the young striker's lofted effort from just outside the box floats over Williams' bar.
7min: Picking up the ball from Josh Brownhill, Watkins turns towards goal and runs inside City's penalty area with purpose before curling a drive wide of Williams' far post.
2min: GOAL - Bradford City 0 Barnsley 1 - The visitors have the lead just as the clock ticks into the third minute of the game. George Williams' cross into the box just evades the head of Rory McArdle, allowing Marley Watkins to nip in and head past Ben Williams.
0min: The Bantams kick off - they will attack towards the T.L Dallas Stand end in the first period.
BRADFORD CITY LINE UP:
Williams, Darby, McArdle, Burke, Meredith, Marshall, McMahon, Routis, Morris, B Clarke, Proctor
Subs: Cracknell, N Clarke, Hanson, Knott, Leigh, Reid, Davies
Bradford City substitutions:
N Clarke for Burke (46), Davies for B Clarke (55), Knott for Routis (71)
Bradford City cautions:
BARNSLEY LINE UP:
Davies, Bree, Mawson, Long, Williams, Watkins, Brownhill, Hourihane, Isgrove, Fletcher, Winnall
Subs: Townsend, Roberts, Scowen, Khan, White, Abbott, Templeton
Roberts for Mawson (19), Scowen for Fletcher (82), Khan for Isgrove (90+2)
Referee: S Hooper
Assistant Referee: G Hilton
Assistant Referee: J Bell
Fourth Official: P Graham