Two poor pieces of defending allowed Paul Ince's visitors to score, initially just before half time and then 30 seconds after Jamie Lowry had given Chesterfield a deserved equaliser after 69 minutes.
In a swirling wind and driving rain, Lee Richardson's side started reasonably well. Jack Lester chipped over the back line to find David Dowson but his left-footed shot was saved by Willy Gueret, diving low to his right.
Janos Kovacs headed just wide from a Lowry free kick and Peter Leven drilled a 20-yard free kick just over the bar and Jamie Winter's quick free kick was returned to him via Dowson and Lester and the Scot's shot was dealt with low down by the keeper.
Dons' opener, their first meaningful sortie into the danger area, saw a cross from Alan Navarro slide past a crowd of blue shirts to fall for Keith Andrews at the far post to tap in a simple goal.
What do you think? Post your comments below. Jamie Ward was introduced as a half-time sub for Dowson and he looked a threat from the off.
He teed up Lester whose 20- yard shot was deflected for a corner before Lester crossed across the face of goal in a similar vein to the goal conceded, but Lloyd Kerry was just unable to latch on to the teasing
delivery.
Lowry's leveller, a 20-odd yard deflected shot, came after Ward, fellow sub Steve Fletcher and Lester had all been involved in a decent build-up and at that point, a home win looked a good bet.
That state of affairs though lasted for just an instant. From the kick-off, sub Aaron Wilbraham received, deceived Peter Hartley and then Kovacs, feeding Lloyd Dyer who shot beyond Barry Roche to halt the comeback in an instant.
Full back Dean Lewington whacked a long-ranger against the foot of the post, the last close call, though Ward almost deceived the Dons rearguard with a brilliant turn away from Jude Stirling and a cross that was hacked away for a corner.
In the final 10 minutes, Chesterfield were unable to break out of their own half as the visitors played an excellent game of keep-ball to frustrate their hosts and the home fans who were desperate for a grandstand finish, but a late leveller never looked likely.
Richardson said: "It was a perfect illustration of our season, a missed opportunity. MK Dons have come here and gone to the top of the league again so they've got something about them. What they do have about them is a belief and an assuredness you get when you've been at the top of the league all season.
"We're young and naïve and a bit daft. We gave them a goal in the first half after I'd been really pleased with the approach and strategy to be patient in defence and it was all going fine until just before half time when we switched off, didn't stick with runners and we conceded a goal, so we went in on a downer.
"We got ourselves back in the game and then have a complete switch-off by a young full back who, in fairness to him, allows a decent pass inside of him, but they should never have been able to do that and we're 2-1 down again after getting back into the game. Another missed opportunity."
Chesterfield must hope tonight's matches go in their favour ahead of Saturday's trip to Millmoor which now has become yet another 'must-win' encounter for the Saltergate side.
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