The League Two champions had opened the scoring late in the first half through Aaron Wilbraham, but Michael Twiss equalised with 12 minutes left to send the biggest home crowd of the season away disappointed.
Nonetheless the Dons were still crowned champions and had a chance to parade the Johnstone's Paint Trophy to their fans.
Both teams seemed to be looking forward to their summer holidays in the first half as neither goalmouth saw much action.
Jemal Johnson turned well and had a shot well saved by Shwan Jalal early on for MK Dons.
In return Carl Baker escaped Danny Swailes in the box but with the goal gaping directed his shot too close to Willy Gueret who toed wide.
It looked like the half would end goalless, but the crowd were finally given something to cheer about on 41 minutes when Johnson went on a mazy run and fed the ball through to Wilbraham who poked home precisely.
Despite the Dons attacking the Cowshed second half they again found it hard to inject any pace into the game, even though they dominated possession.
Swailes headed a Jude Stirling long throw over the bar and John Miles' weak shot past the post were the only efforts.
In reply Baker forced a good save from Gueret with his well directed header from a corner.
They continued to push for an equaliser and were rewarded with 12 minutes to go when substitute Michael Twiss headed home from close range after Danny Adams' knock-down.
Dons should have levelled within minutes when Miles' pass found its way through to Wilbraham but Jalal closed him down well and he fired into the side netting.