Jack Nolan reached double figures for the season but an added time goal secured promotion-chasing MK Dons the win.
Nolan gave the Reds a first half lead as Stanley’s defence limited Mike Williamson’s side.
However a free kick from Jack Payne levelled the game in the 71st minute and then, in the third minute of added time, Joe Tomlinson scored the winner, gutting for the Reds who had battled so hard.
Stanley dropped to 13th place in League Two, five points outside the Play-Offs.
Tommy Leigh and Jay Rich-Baghuelou returned to the starting line-up with Norwich loan defender Lewis Shipley injured.
There wasn’t a lot of goalmouth action in the first ten minutes despite Stanley forcing the early pressure.
Stanley’s opener came on 11 minutes with Nolan getting the ball on the left, cutting inside and firing a shot from the edge of the area which sailed through a sea of players and sneaked into the bottom corner of the net. It was Nolan’s 10th goal of the season.
Stanley suffered a setback when Rich-Baghuelou, after returning from injury, hobbled off on 25 minutes, replaced by Aaron Pickles.
Stanley’s defence was rarely troubled – in fact MK Dons didn’t have a shot in the first half – while Nolan’s goal was the Reds only shot on target.
Seamus Conneely came on at the break for Jake Bickerstaff and it was MK who started on the front foot without seriously testing Radek Vitek.
Kyran Lofthouse fired over the top for MK on 53 minutes with Stanley having the next effort, Josh Woods heading wide on 63 minutes.
The Dons equalised on 71 minutes from a 25-yard free kick when Payne rifled the ball into the top corner past Vitek – the first goal the Man United loanee conceded in his three-game Stanley career.
Substitute Ellis Harrison fired straight at Vitek while, on 78 minutes, Josh Woods sent an effort into the side netting as both sides looked for the winner.
Harrison forced another save from Vitek on 82 minutes and the Czech stopper dived low to keep out a Lewis Bate long range strike.
On 90 minutes, Stanley sub Alex Henderson headed wide at the far post from a Nolan free kick and MK went straight up the other end with Vitek pushing away a Tomlinson strike.
From the resulting corner, the ball came out to Tomlinson outside the area and his long-range effort sailed through a crowd of bodies and beyond Vitek for the winner.
Mk almost grabbed another but the Stanley keeper denied unmarked Alex Gilbey just before the final whistle.
Stanley: Vitek, O’Brien, Rich-Baghuelou (Pickles), Hills, Gubbins, Nolan, B Woods, Martin (Henderson), Leigh, J Woods, Bickerstaff (Conneely)
Subs: McIntyre, Mellor, Quirk, Adekoya
Yellow: Gubbins, Martin, Conneely, J Woods, O’Brien, Nolan, Coleman