Substitute Jabo Ibehre scored his first MK Dons goal to give Paul Ince's side their first win of the season and end Tranmere's long unbeaten home run.
Striker Ibehre, who joined the Dons from Walsall this summer, turned home Jemal Johnson's cross with 10 minutes to go to inflict Rovers' first Prenton Park defeat since October 2008. It was a deserved victory for Ince's side, who showed all the classic away-day traits that led them to a record-equalling 18 away victories during Ince's previous spell with the Club.
And despite continuing to battle a host of injury problems, the men from MK have yielded five points from their opening three League 1 games - without even conceding a goal. Having seen skipper Dean Lewington and defender Mathias Doumbe added to his growing list of absentees following their horrendous clash at Swindon on Saturday, Ince was forced into three changes to his side.
Jabo Ibehre slides home the winner from Jemal Johnson's cross. &nbsp; Sol Davis and Darren Powell came into defence and, with Danny Woodards only fit enough for the bench, Mark Carrington was reintroduced to midfield with Luke Howell dropping into the right-back berth. Unsurprisingly, Tranmere boss John Barnes opted for the same side that beat Gillingham 4-2 three days previously and his side came out predictably confident.
Wide man Chris Shuker, who proved a handful down the right in the first half, showed just how confident on 11 minutes when he took aim from long-range and fired in a long-range dipping volley that Willy Gueret was forced to push round the post. The Dons 'keeper was called into action once more shortly afterwards when Shuker's pinpoint cross found Rovers skipper Ian Thomas-Moore well placed, but his looping header was well pushed over.
Ince's side were beginning to grow into the game, but their progress looked to have been dealt a blow when Powell pulled up lame before the half-hour. Woodards, to his credit, stepped off the bench and into his third defensive position this season, having operated at left-back and right-back already, and looked a more-than-assured partner for David McCracken. Having seen Jason Puncheon rifle their best early chance over after 15 minutes, the Dons were beginning to look increasingly threatening and when Jermaine Easter showed great strength to rob Ian Goodison on the left touchline, Luke Chadwick should have converted the front-man's cutback from 15 yards.
As Tranmere's attacks crashed against the barrier formed by McCracken and Woodards, the visitors continued to create and when Johnson played Easter into the box four minutes from the break, Rovers 'keeper Luke Daniels was forced into an excellent close-range save. Having seen the initiative wrestled away from them, Tranmere came out strongly in the second period and will wonder how they failed to take the lead in a three-minute spell of madness in the Dons box.
Thomas-Moore was the man at the heart of the action and only the width of the post denied him a spectacular opener after 51 minutes - his 30-yard volley crashing off the inside of Gueret's left-hand upright and out to safety. Within minutes, the Tranmere skipper was cursing the woodwork again as Gueret tipped Aaron Cresswell's left-wing cross into his path and his close-range effort rattled the underside of the bar, before McCracken blocked heroically to prevent John Welsh converting the rebound. It was thrilling stuff, but the Dons were not to be outdone and Easter became the latest player to be frustrated by the frame of the goal when his 18-yard snapshot smacked the crossbar on the hour.
Faced with the option of consolidating an away point or pushing for all three, Ince produced an emphatic response with the introduction of Ibehre for the hard-working Carrington and it gave the Dons a new dimension. The six-foot-three-inch target man was a different problem for Tranmere to deal with and, having lost the impressive Goodison to injury just before Ibehre's introduction, the home side lacked the physicality to deal with him.
But it was his poacher's instinct that earned him a winning goal as he made a beeline for the six-yard box after Puncheon had fed Johnson down the left. Sliding in alongside Easter, it was a case of who could get the touch first as Johnson laid the goal on a plate.
An inevitably manic rearguard followed as the visitors clung determinedly to what would be a first victory of the season - Davis clearing brilliantly off the line after substitute Terry Gornell had seen his shot deflect past Gueret. But the defence that has yet to be breached maintained its unblemished record and secured an impressive three points.
Tranmere Rovers (4-4-2): Daniels; Logan, Goodison (Collister 65), Gunning, Cresswell; Shuker, Welsh, McLaren, Mahon (Edds 73); Thomas-Moore (c) (Gornell 73), Curran.
Subs not used: Taylor, Macauley, Barnett, Fraughan.
MK Dons (4-4-1-1): Gueret, Howell, Powell (Woodards 29), McCracken, Davis; Chadwick, Gleeson, Carrington (Ibehre 67), Johnson (c) (Partridge 87); Puncheon; Easter.
Subs not used: Searle, Bridges, Chicksen, Flanagan. Goals: Ibehre 80 Booked: Gleeson, McCracken, Howell, Ibehre.
Referee: Jon Moss (West Yorkshire)