New boss Danny Wilson left without comment and looks to have his work cut-out with the relegation threatened Dons who were second best from start to finish but it was a great result for Rovers who bounced back in fine style following their embarrassing 4-0 home drubbing against Sheffield Wednesday the previous week.
Doncaster received a helping hand when they snatched the lead in the ninth minute thanks to a disastrous own goal.
Visiting right-back Gareth Edds tried to turn the ball back to his keeper but Matt Baker had come rushing out of goal and it flew past him into the net.
It was a nightmare debut from Baker playing his first match after signing from Wrexham and he looked far from confident throughout.
Doncaster had made five changes from their starting line up following their defeat by the Owls and it paid off with manager Dave Penny switching Johnson from the flank to a central striking role.
Rovers should have had more goals to show for their first half dominance but James Coppinger hit the side netting and Paul Green had another effort disallowed for off-side.
But Johnson, on-loan from Leeds United made no mistake in the 60th minute when he slid in to make it 2-0 from close-range following good work from John Doolan and Green.
The third goal a couple minutes later was a classic and followed a superb move involving a dozen passes.
Michael McIndoe provided the final ball from the left and Johnson raced through again to fire home in fine style. The on-loan striker was unlucky not to register a quick fire hat-trick when he fired home only to have the effort disallowed for off-side.
MK Dons never looked like fighting back and were fortunate not to lose by a wider margin with Baker saving from Ricky Ravenhill from point blank range in injury time.