The Bantams arrived at Griffin Park fielding a somewhat 'second string' starting 11 that featured players returning from injury and youngsters such as Scott Brown and Forrayah Bass.
City fought bravely to take a strong Brentford side into extra time but the introduction of key players off the bench by Uwe Rosler proved decisive as they eventually proved too strong.
In the early stages it was the hosts that were making all the groundwork and inside the first 5 minutes Stuart Dallas got the better of Rory McArdle to find an opening but his low shot was well saved by Jon McLaughlin.
Fulham loanee Marcello Trotta was the next to test McLaughlin when he latched onto Sam Saunders' through ball to fire an angled shot towards goal but again he was on hand to deal with the effort.
Rosler's men kept pressing and a long ball over the top was expertly cut back by Jake Bidwell and Paul Hayes side footed a shot from inside the area that fizzed marginally wide of the bottom corner with McLaughlin able to little to get near the attempt.
Youngster Scott Brown came a matter of inches away from scoring a spectacular first professional goal. Kyel Reid's corner was only half cleared and Brown lashed a full volley from 20 yards that was close to breaking the deadlock.
Against the run of play somewhat, City took the lead. Leon Legge was caught napping in possession of the ball and Zavon Hines nipped in to dispossess him; he raced into the area before cutting inside, his eventual shot was blocked but Kyel Reid was on hand to slam the ball in from close range to score on his return from injury.
Brentford carried on pushing for a goal and they were coming ever closer to getting it. A corner was half cleared by Ricky Ravenhill, Jonathan Douglas headed the ball back into the mix and Paul Hayes volleyed over the bar.
On the stroke of half time the hosts levelled up the tie. Trotta cut inside from the right to emerge in the area and he was brought down by the stray leg of Carl McHugh. A penalty was awarded and it was the Italian himself who sent McLaughlin the wrong way to equalise.
The second half was to provide The Bantams with a firm challenge and Paul Hayes almost put Brentford ahead; Douglas' angled ball found Stuart Dallas who hit a low cross into the area that had just too much pace to be met by the former Charlton striker.
Blair Turgott showed flair to burst forward and cut inside away from a couple of challenges and hit a ferocious shot from 20 yards that flew only a yard or so wide of the target.
Paul Hayes was presented with yet another chance and this time it came from a set piece. Sam Saunders' corner was met by the head of Hayes but he couldn't force McLaughlin into a save as the ball went over the bar and to safety.
Substitute Adam Baker tried to test Antoine Gounet with an attempt but after a neat turn his pot shot from 20 yards lacked venom and direction and was comfortably dealt with by the French stopper.
Brentford were the width of the crossbar away from winning the tie with 10 minutes remaining after Clayton Donaldson had found Shaleum Logan with a neat flick on, Logan found space in the area to rifle a shot back off the crossbar.
In the dying seconds of normal time Ricky Ravenhill almost grabbed an unlikely winner when he fired a low shot narrowly wide of the bottom corner with Gounet struggling to get there. This was the last of the action in 90 minutes and so the tie headed to Extra-Time.
Four minutes into the additional half an hour The Bantams went ahead. As Blair Turgott produced a cross into the area he was brought down by a late challenge from Shaleum Logan and ref G.Scott awarded a spot kick. Former Brentford forward Alan Connell dispatched it brilliantly to put his side in front once again.
City's lead was held for only 8 minutes though as Brentford equalised just before the half was out. Harry Forrester did well to produce a cross into the crowded penalty area which was tapped home by Marcello Trotta for his second of the game.
Harry Forrester got himself another assist a mere 90 seconds later as Brentford went ahead for the first time all evening. His neat pass found Donaldson who held off Rory McArdle before firing home from a tight angle.
Only 2 minutes later the game was put beyond all doubt with a 4th goal for Rosler's men. The impressive Harry Forrester was again at the centre of things but this time he got himself on the scoresheet. He ran at Ritchie Jones before finding half a yard on him in the area to blast a shot into the far corner from a tight angle and confirm his side's place in The FA Cup 3rd Round.