Reds suffered a fourth successive defeat on a frustrating afternoon at Stadium MK in Sky Bet League One.
A goal down to Dele Alli’s 16th-minute goal, they had a great chance to equalise on 68 minutes when Izale McLeod was brought down by Kyle McFadzean, who was shown a straight red.
But Dons’ keeper David Martin saved the penalty and the ten men clinched the points in stoppage time from Benik Afobe.
John Gregory made one change to the side beaten by Norwich in the Capital One Cup on Tuesday with Gavin Tomlin coming in for Lewis Young. A full bench included goalkeeper Jamie Ashdown, who joined the club on Friday, and Matt Harrold, for the first time in a League game after his recovery from knee surgery.
Will Grigg, who scored twice in Dons’ midweek cup win over Manchester United, was on their bench. Their starting line-up did include ex-Reds’ defender McFadzean.
If the home fans expected something of a hangover following their side’s midweek exploits there was no evidence of it in a one-sided first 30 minutes when Reds were fortunate just to concede a single goal.
Ex-Red Danny Powell had already hit the post while Afobe forced Brian Jensen into an excellent save when MK took a 16th-minute lead when ALLI found a pocket of space on the edge of the box and curled a low shot inside the right-hand post, giving Jensen no chance.
Reds suffered another blow moments later when Bobson Bawling limped off to be replaced by Emmett O’Connor.
Afobe threatened again with a shot on the turn which flew wide and it wasn’t until the 31st minute that Dons’ goal was seriously threatened. Tomlin did well to turn inside the box and get his shot away but it was blocked by Antony Kay.
McLeod was inches away from getting a decisive touch on Gwion Edwards’ cross as Reds began to build some pressure towards the end of the half.
But MK were still a serious threat and after a neat exchange between Powell and Afobe, George Baldock completely mis-kicked 15 yards out and Reds were able to clear.
The visitors were first to threaten after the break when O’Connor’s cross from the right was met by a firm header from Tomlin which went over the bar.
Both sides had spells of possession without either keeper being forced into serious action before the game exploded into life on 68 minutes.
McLeod got goalside of McFadzean as he latched onto a long ball and the former Crawley defender brought him down inside the box. McFadzean was shown a straight red by referee Mark Heywood but McLeod’s penalty down the middle was kept out by Martin’s trailing right leg.
It was a let-off for the hosts which they nearly exploited straight away as they broke forward and Jensen had to make an excellent save from Afobe, who then saw his free-kick from the edge of the box pushed onto the post by Jensen.
At the other end Martin made an excellent save from Henderson’s long-range effort and as Reds probed for an equaliser both Ryan Dickson and O’Connor failed to get shots away from promising positions inside the box.
With 10 minutes to go MK were content to hold what they had and try to counter-attack. Afobe stung Jensen’s palms with a powerful drive by which time Harrold had come on to make his first League appearance for Crawley.
They had a golden chance to equalise in the 84th minute when O’Connor played Dickson’s deep cross back into the six-yard box but Martin made a reflex save from Tomlin’s close-range effort.
But it was the home side who sealed victory in stoppage time. Arsenal loanee AFOBE used his pace and power to pick his way through the Crawley defence and fired past Jensen and inside the far post.
Reds: Jensen; Oyebanjo, Leacock, Walsh, Dickson; Edwards (sub: Harrold 77), Henderson, Smith, Bawling (O’Connor 18), Tomlin, McLeod. Unused subs: Ashdown, Bradley, Young, Banya, Rose.