Wrexham simply had no answer to the blistering speed and skills of MK Dons substitute Izale McLeod who notched his seventh goal of the season and transformed the game in the process.
He came on at the start of the second half and, with a smart move down the middle, took the ball on the turn and left keeper Michael Ingham a spectator as he smashed home to level.
He was responsible for the winner too in the 77th minute, whipping down the right flank and his pin-point cross found Sean O'Hanlon at the far post to score from close range.
It would have been a travesty had the visitors not won because near the end Chris Llewellyn and Matt Done came close to getting levellers.
Wrexham were handed a blow when they lost their rugged striker and skipper Neil Roberts and then central defender Steve Evans through injuries.
It was Roberts who shocked MK Dons on 20 minutes following a goalmouth scramble as he hit the ball past Adolfo Baines-Pilart although the keeper did get a hand to it.
Clive Platt, who thought he'd grabbed a first minute penalty, came close on 28 minutes with a free-kick which flashed past the target.
Then Scott Taylor held his head in his hands when he flashed a shot against the post.
Wrexham were having difficultly in coping with the Dons' quick bursts by Platt and winger Lloyd Dyer.
Manager Martin Allen brought on McLeod for Taylor at half-time and he was an instant hit despite his goal.
He showed pace and skill down the flanks which Wrexham simply couldn't handle.
Just before O'Hanlon's winner, Baines-Pilart made a match winning save when he somehow kept out an effort from Wrexham's rising star Mark Jones.
Then Wrexham were caught by another speedy attack by the Dons which saw McLeod's cross tucked home by O'Hanlon.