Lightening fast striker Izale McLeod struck twice in 60 seconds to earn MK Dons their first League One away victory after Rovers led at half-time.
It was a thoroughly deserved success and the margin could have been greater.
But Tranmere were left kicking themselves late on when substitute Calvin Zola missed the target from eight yards when he should have done much better.
McLeod gave Tranmere a warning in the 33rd minute when he brought an excellent save from John Achterberg.
Rovers then seized the initiative and skipper Mike Jackson headed home in style in the 39th minute from a free-kick by Steve Jennings.
The visitors levelled from the penalty spot in the 57th minute. McLeod was floored by Ian Sharps and picked himself up to send the keeper the wrong way and place his kick into the bottom right hand corner.
Straight from the re-start Tranmere gave away possession and Clive Platt sent McLeod clear to round the keeper and net the winner.
There was no way back for Rovers as they failed to win at home for the sixth time in eight matches and the pressure on manager Brian Little is now mounting.