A late goal from Stephen Gleeson gave MK Dons all three points at Prenton Park on Friday night.
The MK Dons midfielder struck with just minutes remaining of a match dominated by the visitors.
Ronnie Moore made three changes to the team that started at Braintree Town as Adam McGurk, Jake Cassidy and Liam Palmer came in for Joe Thompson, Cole Stockton and Danny Harrison. Former Tranmere captain Antony Kay started for MK Dons.
Dean Bowditch shot high over Owain Fon Williams' cross bar on three minutes and four minutes later the visitors should have taken the lead. Ryan Lowe got through the Rovers defence after a mistake from Ash Taylor but when one on one with the keeper he shot wide of the target from 20 yards.
Tranmere's first chance came on nine minutes when McGurk's inswinging free kick just evaded Jake Jervis at the far post while Fon Williams kept out Luke Chadwick's volley at the other end soon after.
On 20 minutes a Stephen Gleeson shot was blocked and Darren Potter fired inches past the right hand post from the follow up 25 yards out.
After McGurk raced clear on the left and curled beyond the right side of the net with his right foot, a free kick from Dean Lewington had to be tipped over by Fon Williams.
Cassidy miss hit a shot from close range after being picked out by Wallace on 27 minutes while Lewington and Chadwick both missed with efforts for the visitors before half time.
Danny Harrison replaced Jake Jervis at the start of the second half and immediately went about trying to deny Dons attacking midfielder Chadwick time on the ball.
A couple of early breaks for Jake Cassidy were ended by the officials for offside and a foul while a shot from Palmer was blocked by Kay on 50 minutes.
Kay popped up at the other end to head wide form Dean Bowditch's chipped cross on 54 minutes, four minutes before former Manchester United striker Alan Smith replaced Lowe.
A low strike from Wallace from 25 yards out forced Martin to palm the ball away from the bottom right corner on 60 minutes while Wallace was in the right place at the right time to clear Dean Lewington's header from the goal line eight minutes later.
A lofted pass from Wallace picked out Bakayogo on the left wing on 75 minutes but Cassidy was ruled to be offside from the cross that followed.
After Fon Williams had saved from Shaun Williams, Kay fired over the Tranmere bar from outside the area.
A 20 yard shot from Cassidy went wide of the target on 85 minutes but soon after the visitors took the lead. A shot from Bowditch was parried by Fon Williams and Gleeson was closest to the loose ball, rolling a shot across the line from close range.
The Dons survived a goalmouth scramble as Rovers looked for an equaliser and it was the closest the home side came to levelling before the final whistle
Tranmere: Fon Williams, Holmes, Taylor, Gibson, Bakayogo, Robinson, Wallace, Palmer, McGurk (Stockton 90), Cassidy, Jervis (Harrison 45 HT). Substitutes: Mooney, Kay, Goodison, Power, Kirby.
MK Dons: Martin, Otsemobor, Lewington, Williams, Gleeson, Potter, Bowditch, Lowe (Smith 58), Kay, Chadwick (Doumbe 90), Balanta (Powell 65). Substitutes: McLoughlin, Chicksen, O'Shea, Sekajja.
Referee: Michael Naylor
Yellow cards: Jervis (24)