MK Dons were the better side throughout with the visitors' inability to deal with crosses again severely highlighted.
Sean O'Hanlon and Aaron Wilbraham converted corners in the first half before Robert Snodgrass reduced the deficit after the break.
But Wilbraham headed the Dons' third goal six minutes later as they made it seven wins from their last eight games.
Roberto di Matteo's side scored two early goals but it could have been very different had Leeds converted an absolute sitter in the opening minutes.
Neil Kilkenny turned and hit a rasping volley that was palmed away by Willy Gueret before Luciano Becchio and Robert Snodgrass got in each other's way with the former somehow blasting wide from point-blank range.
That turned out to be Leeds' only real chance of the half as, after 11 minutes, the home side took the lead.
The visitors' inability to defend corners was embarrassing in the first half and, from Jemal Johnson's ball, O'Hanlon stopped low to head home at the near post.
Then, six minutes later and from the same side, Johnson whipped in another cross. There was an almighty scramble with Wilbraham eventually poking the ball in from close range.
The rest of the half was a non-event as the travelling Leeds fans got on their team's backs, making United nervous on the ball.
The Dons on the other hand looked more than comfortable and could have had another goal on the stroke of half-time when Wilbraham's header across goal from Shaun Cummings' cross just went wide.
Leeds needed an early lift in the second half and they got one, Snodgrass volleying in a peach of a goal after the Dons had failed to clear a cross.
But, after having a decent penalty shout waved away minutes later as Snodgrass hit the ball against Miguel Angel Llera, they shot themselves in the foot when they conceded from another cross.
Again the provider was Johnson as his inviting ball was flicked in with aplomb by Wilbraham.
Leeds' heads again dropped and, despite a few half-chances, including a Luciano Becchio overhead kick that just went wide, they never looked like earning something from the game.