Veteran striker Kevin Gallen notched the winner to send MK Dons up to fourth in the League One table.
Tranmere's Charlie Barnett had the first decent attempt with a shot from 18 yards but Antony Kay and Ben Chorley had to be alert to keep MK Dons at bay.
The home team started the second period well as Jason Puncheon and Luke Chadwick had powerful shots blocked.
But late substitute Gallen broke the deadlock after he scored almost instantaneously from Puncheon's corner.
This page is best viewed in an up-to-date web browser with style sheets (CSS) enabled. While you will be able to view the content of this page in your current browser, you will not be able to get the full visual experience. Please consider upgrading your browser software or enabling style sheets (CSS) if you are able to do so.
Bookmark with:
What are these?