Izale McLeod was the main culprit, missing three golden opportunities before Dons skipper Paul Mitchell and manager Danny Wilson saw red late on.
Wilson named the same team that drew 1-1 at Walsall, with Gareth Edds continuing in right midfield in place of the injured Wade Small and Leon Crooks deputising for Trent McClenahan at right-back.
Milton Keynes dominated the early exchanges and after Stephen Quinn had been tripped by Gareth Davies on the corner of the box, Nicky Rizzo's dangerous free-kick was headed over his own crossbar by Reuben Hazell in the fifth minute.
Edds forced Chesterfield goalkeeper Barry Roche into a decent save with a long-range half-volley from a well worked Rizzo corner before McLeod's misses.
First he swivelled in the box and fired just past the post, then he pulled an effort badly wide from the edge of the box after neat set-up play by Quinn, before the 21-year-old missed an absolute sitter in the 19th minute.
Rizzo's through ball set McLeod clear, but after his first effort was saved by Roche, he somehow fired the rebound against the post from just four yards before Edds' bundled follow-up was cleared off the line by Hazell.
Dons continued to pile on the pressure in a one-sided first half and Quinn hit the outside of the post with a snap-shot from 12 yards after good work on the right by Edds.
Chesterfield's best chance fell to Colin Larkin who nipped in to cut out Craig Morgan's weak back pass but clipped his effort wide from an angle.
And then Shane Nicholson's 41st minute quick free-kick almost caught out goalkeeper Matt Baker as the visitors improved towards the end of the half.
But the Dons took control after the break and after Davies had felled McLeod on the edge of the box, Rizzo's curling 51st minute free-kick came back off the post with Roche struggling to reach it.
Mitchell's through ball set McLeod away again in the 62nd minute but his touch was too heavy and Roche was quick off his line to smother.
Mitchell, who was yellow carded in the 61st minute for kicking the ball away, was given his marching orders nine minutes later for persistent offending after bringing down Chesterfield substitute Sammy Clingan in his own half.
The Spireites came back into the game with their numerical advantage but the best they could muster was Derek Niven's long range strike that Baker tipped over acrobatically.
Dons boss Wilson was sent to the stands late on by referee Trevor Parkes as tempers boiled over.