Luckless Rovers found little going right as they fell to a fourth defeat on the spin, but the Milton Keynes club are up to third after a fifth straight win.
The early play was scrappy. Robbie Weir, Jose Baxter and Enoch Showunmi had no luck with headers for Tranmere before the Dons went in front with their first chance after 19 minutes. A smart counter attack saw Jabo Ibehre head in at the far post from a cross by Adam Smith.
Showunmi only just missed the target for the Merseysiders two minutes later before David Martin in the Dons goal made good saves from John Welsh and Baxter.
Luke Chadwick fired wide for the visitors after good approach work in the 39th minute. Then on-loan keeper Paul Rachubka did well to block a close-range strike by Ibehre. At the other end, Martin held on well to an Andy Robinson free-kick.
It needed a terrific fingertip save by Rachubka to deny Chadwick a second goal, but the visitors did double their lead on the hour with a low strike by Shaun Williams. Baxter struck the bar with a 65th minute free-kick for Rovers and from the rebound Showunmi somehow blazed over from three yards out.