Leeds made it five defeats in a row a result that ultimately cost boss Gary McAllister his job.
Leeds gave a debut to new signing Mansour Assoumani at right back hoping that he would be able to help sort out their defensive frailties.
The Whites nearly took an early lead when Howson`s shot was fumbled by the Dons keeper and Robert Snodgrass followed up but his shot went across the face of goal.
Leeds defensive frailties were soon exposed, a corner was swung in low and O`Hanlon got his head to it almost on the ground and from an acute angle it somehow managed to find the back of the net.
The lead was soon doubled when from another corner Leeds failed to clear their lines and Wilbrahim pounced to poke the ball into the back of the net.
Leeds tried to get back into the game and Assoumani forced Gueret into a good save in the MK goal.
Soon after Jonathan Douglas and Lubo Michalik went close for Leeds but neither of them could beat Gueret.
Milton Keynes went in at half time the much happier of the two sides with a two goal lead.
The home side nearly increased their lead at the start of the second half when Puncheon`s shot clipped the top of the bar.
Leeds finally found the back of the net early in the second half when Snodgrass fired a sweet left foot shot into the corner of the net to give Leeds hope.
Straight after the goal Leeds felt they had strong claims for a penalty for handball but the referee waved away Leeds protests.
The hope was to be short lived though when Wilbrahim got up well above the Leeds defence to restore Milton Keynes two goal advantage.
Leeds continued to try to get back into the game and efforts fell to Marques, Becchio and Showunmi all having chances but failed to find the back of the net.
The final whistle went much to the delight of the home side, the result sees Leeds drop down to ninth place and they must somehow now find their form when coming up against top of the table Leicester City on Boxing Day at Elland Road.
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