Daniel Harvie's strike 14 minutes from time was enough for the hosts to claim all three points and extend Rovers' winless run to five games.
The defeat means that Doncaster have picked up just two points from the last 15 on offer but their play-off destiny still remains in their own hands.
Despite being outside the top six, Andy Butler's side have played fewer games than most of the sides above them.
However, the table remains very congested below them and they need to quickly rediscover their winning form if they are to prevent themselves sliding down the ladder.
Butler made three changes from the side that started in the 2-2 draw with Gillingham a week ago.
John Bostock, Jason Lokilo and Taylor Richards were named in the starting 11 in place of Matt Smith, Fejiri Okenabirhie and Josh Sims.
Smith is on international duty with Wales while Sims is back with parent club Southampton for an assessment on his left leg.
The visitors had goalkeeper Louis Jones to thank for the game remaining goalless at the break.
Rovers failed to test Andy Fisher much at the other end. James Coppinger was played through midway through the first 45 minutes but the MK Dons goalkeeper was out quickly to force the Doncaster man away from goal.
Jones made a trio of fine saves in the first half. Firstly, he got down well to his left to claw away a header from Will Grigg who had done well to generate some power and accuracy behind the shot.
Daniel Harvie's effort from outside the box was then tipped onto the post by Jones before the ball rolled across the line and the rebound was turned behind for a corner.
From the resulting set-piece, the ball found its way to Zak Jules who drove a low effort just wide of the post.
Grigg was denied for a second time when he opened his body up to create space for a shot eight yards out but the ball was kept out by another smart stop by Jones.
Doncaster were able to muster more of an attacking threat in the second half. Jason Lokilo was played in by Omar Bogle but saw his shot well blocked by Harry Darling before he fired the loose ball over the crossbar.
Neither side was able to fashion any big openings until Harvie found the back of the net on 76 minutes. Jones was left unsighted by Joe Wright, who had flung his head at the ball attempting to clear, as MK Dons celebrated.
Lokilo drew a simple save from Fisher in the closing stages but it was a tame effort as Doncaster travelled back home empty handed, a familiar theme in most of their recent away outings. Their last away victory remains a 1-0 success at Lincoln City on January 30.
MK Dons: Fisher; O’Hara, Darling, Jules; Harvie, O’Riley, Surman (Laird 67), McEachran, Sorinola (Jerome 67); Fraser (Thompson 28); Grigg (Brown 83). Subs: Nicholls, Lewington, Mason.
Doncaster Rovers: Jones; Halliday, Wright (John 81), Anderson, Horton (Gomes 80); Bostock (Robertson 80), James; Lokilo, Richards, Coppinger (Okenabirhie 64); Bogle. Subs: Balcombe, Amos, Greaves.
Referee: J Smith (Lincolnshire).
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