The Dons took the lead with a 74th minute penalty, but it was clawed back eight minutes later by the Merseysiders who were dropping home points for the second time in the week.
The visitors could not capitalise on a bright start and it was Tranmere's Charlie Barnett who brought the first save of the game from Willy Gueret after seven minutes. Then Chris Shuker had a shot blocked after good home approach play.
Peter Leven appealed in vain for a penalty when he appeared to be pulled back by Ben Chorley on 26 minutes. A minute later Alan Navarro put a 25-yard drive just wide of the home goal.
At the other end Barnett was again out of luck with a wayward volley as the ball bounced about inside the box.
But generally the first period developed into a dogged midfield battle with no quarter given and precious little entertainment.
Tranmere almost sneaked ahead in the 44th minute with Gueret doing well to tip an angled Shuker effort away for an unproductive corner.
The home side gained no reward for a lively start to the second period and the first real goal action came on 54 minutes when Miguel Llera headed wide for the Dons following a Jemal Johnson free-kick.
Navarro collected the only caution for a foul shortly after the hour mark.
Dons broke the deadlock with a 74th minute penalty from Leven, after Aaron Wilbraham was tripped in the box by Antony Kay after a Johnson free-kick.
Tranmere sent on three subs and were rewarded on 82 minutes. A Shuker corner was headed goalwards by Kay and Terry Gornell flicked home from close range.
Llera was excellent in central defence for the Dons and Jason Puncheon and former Rover Navarro worked hard in midfield.
Barnett and Shuker were generally in the thick of the action for the Merseysiders.