After being in control for the whole game they inconceivably conceded twice in four minutes late on.
They had cantered in to a 2-0 lead with goals from Aaron Wilbraham and Jason Puncheon.
They had further chances to extend their lead as Crewe never looked like scoring, until the 78th minute, when Mark Carrington headed home superbly.
Then Willy Gueret brought down Alan Sheehan minutes later with Gylfi Sigurdsson sending the keeper the wrong way from the spot.
After a rapid start the Dons were able to cruise through the first half at walking pace.
Inside ten minutes Luke Chadwick should have given the Dons the lead when Wilbraham held the ball up well and set the winger through on goal only for him to brush the side-netting with his strike.
But then, on the quarter-hour mark, they went one better. Puncheon picked up the ball 30 yards out and faked to shoot before playing in a slide-rule pass for Wilbraham whose shot took a wicked deflection off Marlon Broomes and sailed over the helpless John Ruddy.
Four minutes later the Dons were gifted a second goal. This time Wilbraham played a clever first-time ball for Puncheon on the halfway line and he drove to the edge of the box before hitting a weak shot straight down the middle that Ruddy somehow let through his legs.
With Crewe's heads down and unable to keep the ball for more than ten seconds, the Dons played the rest of the half with ease, mostly passing the ball back and forwards between the defence.
There were a few fleeting glimpses of life. Puncheon forced a save from Ruddy and then, on the stroke of half-time, Peter Leven fired over from the edge of the box.
The second half was more lively, but then it had to be. A speculative early throughball found half-time substitute Jemal Johnson, who had replaced Chadwick.
After Danny Woodards could only get a toe to the ball, Johnson cut in past the centre-half but fired straight at the keeper. However, the ball fell to Baldock but, from an incredibly tight angle, he could only fire against the post.
Then a great break through the middle by Puncheon saw him fire a shot that was deflected into the grateful arms of the already grounded Ruddy.
Then, just before the hour, a bizarre thing happened as Crewe finally forced a save from Gueret as Sigurdsson twisted and turned on the edge of the box before hitting a low shot towards the far post.
On the hour Johnson raced through on goal and looked destined to score until Woodards made good ground to make a superb saving challenge to save a sure goal.
Minutes later Baldock cut in down the left and played a teasing cross to the back post for Wilbraham who controlled but then sliced wide.
A howler down on the right from Carl Regan almost gifted Crewe a goal as he gave the ball away cheaply to Byron Moore whose cut-back was inches away from the boot of Clayton Donaldson.
Then, with 12 minutes left, the unthinkable happened as good work from Moore on the right ended with him perfectly curling the ball in for Carrington whose lovely glancing header gave Gueret no chance.
Four minutes later the Dons really hit the self-destruct button as a quick break ended with Donaldson playing in Alan Sheehan who was then clipped by the onrushing Gueret with the referee having no hesitation in awarding a penalty.
Gueret was then sent the wrong way by the clinical strike of Sigurdsson from 12 yards as stadium:mk was left silenced.
Three minutes from time the Dons' players claimed vehemently for a penalty after a corner but among a crowd of bodies it was hard to give and they never looked like getting their lead back as Crewe were buoyant.
In stoppage time they could have stolen the win when Sigurdsson's 30-yard free-kick was spilled but he recovered to block Donaldson's follow-up effort.