The hosts failed to take advantage after dominating most of the match and were made to pay late on as Lowe, who scored twice against the Dons last October, snatched the points for Rovers.
MK Dons had the first opening after four minutes when Ben Reeves’ effort from the edge of the area was turned away by Tranmere goalkeeper Owain Fon Williams.
Daniel Powell then spurned a great chance when he lifted the ball over the crossbar after he had been excellently played through by Samir Carruthers as the first half finished goalless.
The Dons continued to press after the break with Carruthers sending a long-range strike just wide of the far post.
But Rovers hit their hosts with the sucker-punch in the 90th minute when Jake Cassidy got in behind down the left and cut the ball back for Lowe to tap into an empty net.