Bradford had frustrated the hosts for most of the match, but strikes from Keith Andrews and Danny Swailes ensured the Bantams' fourth straight defeat, before substitute Barry Conlon's last-gasp consolation from the penalty spot.
Milton Keynes dominated the first half but Bradford threatened on the counter-attack and David Wetherall thought he'd given the visitors the lead in the 25th minute, only to see his strike ruled out for a push on Swailes.
Wetherall tapped in the rebound from close range after Dons keeper Willy Gueret had saved Mark Bower's header from Paul Evans' free-kick, but his joy turned to despair when he saw the assistant referee flagging for his shove on the centre-half.
Dons midfielder Alan Navarro a curled a 25-yard effort just wide before his dangerous low cross was turned wide by the stretching Aaron Wilbraham at the far post in the 35th minute.
Bradford, set out in a defensive 4-5-1 formation, were happy to sit back and continue their strategy of soaking up the pressure in the early stages of the second half.
And the ploy seemed to be working as the frustrated hosts huffed and puffed without reward against the Bantams' disciplined back-four.
Bradford survived a strong penalty appeal in the 70th minute as a cross from Leon Knight, who was largely ineffective, appeared to strike full-back Darren Williams' hand from three yards, but referee Fred Graham gave him the benefit of the doubt.
But Milton Keynes weren't to be denied and Andrews finally broke the Bantams' dogged resistance in the 73rd minute.
Wilbraham perfectly cut back Dean Lewington's deep cross into the path of the on-rushing Andrews, who coolly stroked his seventh goal of the season inside the far post from the edge of the box.
Knight could have made it 2-0 moments later but he mis-controlled Andrews' incisive through ball as the ball ran away from him and into Rhys Evans' grateful arms.
But the unmarked Swailes did double the Dons' lead in the 81st minute, firing in his second goal of the season from eight yards after Drissa Diallo had hooked the ball back into the danger zone with an acrobatic over-head kick.