An injury-time goal secured all three points for MK Dons after Accrington Stanley had come back from 2-0 down.
The Reds were 2-0 down on 55 minutes after Russell Martin’s side had dominated the chances.
But two goals in five minutes – a Dion Charles strike and an own goal – got the Reds back on track.
However Matt O'Riley headed home in the 92nd minute to make it successive defeats for John Coleman's men.
Charles passed a late fitness test to start for the Reds with Seamus Conneely, Colby Bishop and Nathan Baxter still out injured, along with a host of other longer-term injured players.
MK Dons, who had four losses in their previous five games, made a dream start on six minutes when Matthew Sorinola’s spinning ball forward found Cameron Jerome in the area and he took the ball down, turned and slotted home from a tight angle.
Jerome had a chance to put the Dons 2-0 up on 15 minutes with his initial shot blocked by David Morgan and his follow-up saved by Toby Savin.
Stanley suffered another blow in the 16th minute when Matt Butcher went off injured, replaced by Adam Phillips.
Jerome headed into the side netting from a tight angle and had a fifth chance pushed behind by Savin.
Scott Fraser forced another save out of Savin which Mark Hughes got back to clear as the home side dominated the first half chances.
Stanley came more into it towards the end of the half. Paul Smyth had a shot collected by goalkeeper Andrew Fisher and then striker Smyth almost capitalised on a goalkeeper error but the Dons managed to clear for a corner.
Charles had a chance blocked early in the second half while O’Riley tricked his way into the Reds’ area but he was dispossessed.
Stanley appealed for a penalty on 52 minutes as Phillips was felled under a challenge on Fisher but nothing was given.
And MK Dons soon doubled their advantage on 55 minutes. Sorinola’s ball in from the left found Jerome, who got in front of the defence to poke home his 14th goal of the season.
However two goals in five minutes got the Reds back all-square.
On 57 minutes, the MK Dons didn’t clear the ball, Ben Barclay played the ball back from the by-line to Charles who fired home his 17th goal of the campaign.
It was 2-2 on 62 minutes when a Sean McConville corner found Barclay, he stroked the ball goalwards and it got a final touch off Don's midfielder Andrew Surman to wrong foot Fisher.
Sorinola fired over the bar in a decent position while O’Riley’s free kick deflected wide with nine minutes to go.
With two minutes of injury time on the clock, another Sorinola ball in found the head of O'Riley who secured the win for MK Dons.