Jason Kennedy's first goal of the campaign with time running out at stadiumMK finally sealed the points for Parkinson's men after they had twice taken the lead earlier in the match.
The victory ended a recent winless spell for the Bantams and moved them back up into the Play-Off places in the League 1 standings.
The positive result - City's third away win of the season so far - also now means the Bantams have only lost once in their last five league matches.
Parkinson said: "It has to go down as the biggest win of the season to date for us.
"Although we have still been playing well recently, we haven't had that win. We needed to get one to get us back going again, and we've got it with a really spirited display.
"Our defence, at times, was at full stretch. But, with the make-up of our team being so attacking in terms of two out-and-out wingers and two strikers up top, the back four is going to come under pressure. On the whole though, they did really well up against some good players.
"We started slowly in fairness and got our first goal against the run of play. It is a great cross from Tommo (Gary Thompson) and a great finish from Nahki though to get us that lead.
"MK Dons always looked dangerous, however, and they're got their equaliser before we've gone back in front again.
"I thought in the start of the second half we were excellent and we had some great chances to go and get the third goal.
"When we didn't get it, you start to think 'are we going to get punished?'.
"It's taken a penalty to get them back in it, but the way we scored our third goal just sums up this group of players.
"(Mark) Yeatesy has come off the bench and shown a little bit of quality. (James) Meredith has driven up on the outside so late in the game and crossed it across goal for Jason Kennedy, who must have been tired because he hasn't played for a while but still got himself into the six yard box to get us the win."
Kennedy's match-winner was his first for the club in only his second league start of the season. The midfielder came into the side at the expense of Nathan Doyle, and his late winning goal capped off a pleasing performance from the former Rochdale player.
Parkinson added: "He's come in and done really well today (Saturday).
"I am really pleased for him because he is a good player and it is nice for him to get the opportunity to show the fans that.
"He's a strong player, who competes in midfield and also passes the ball. He has a lot of energy to his game.
"That moment at the end (scoring the winning goal) will do him and the whole squad the world of good because it's vital that when a player comes in, they make an impact."