Headers from Pawel Abbott Andy Booth put the Terriers 2-0 up, but two goals in two minutes from substitute Nicky Rizzo and Izale McLeod put the Dons level before David Mirfin and Chris Brandon saw red for the visitors in the 90th minute.
Dons boss Danny Wilson made one change to the team that beat Southend 2-1 in the FA Cup second round on Saturday, with playmaker Gary Smith coming into the line-up for Gareth Edds.
Dons started brightly and Smith slotted Wade Small through inside the first minute but his poor control let him down before Dean Lewington's cross-cum-shot was clawed over the bar by Paul Rachubka.
But the Terriers hit back in a lively opening and after Booth's powerful strike was magnificently tipped round the post by Matt Baker, Abbott capped his return to the starting line-up after injury with his 12th goal of the season after seven minutes.
Brandon picked up a loose ball on the left and crossed perfectly for Abbott to thump home a powerful header off the post from 10 yards.
A terrible goal kick by Baker almost gifted Abbott his second on the stroke of half-time, but the keeper redeemed himself for slipping over by turning the left-foot strike around the post after he raced clear on goal.
The Dons came out fired up for the second half and were unlucky not to be awarded a penalty six minutes after the re-start when Gary Taylor-Fletcher appeared to handle Trent McClenahan's cross in the box.
The Terriers caught Milton Keynes on a swift counter-attack as Booth put them 2-0 up in the 64th minute.
Danny Adams crossed from the left and Booth, one of three players left unmarked on the edge of the six yard box, headed his ninth goal of the season on his 32nd birthday.
At the other end McLeod nipped in ahead of Mirfin on to a long ball but Rachubka was quick off his line to block, before substitute Rizzo gave the hosts hope with a cracking 81st minute free-kick.
Rizzo stepped up after Smith had been fouled by Adams on the edge of the box to whip a fantastic 22-yard strike around the wall and into the top corner.
And then just two minutes later McLeod capped a magnificent comeback with the equaliser.
Smith drilled in a low cross and McLeod was left unmarked to convert his 10th goal of the season from 10 yards, before Mirfin was shown his second yellow card for bringing down Smith on the edge of the box in the 90th minute.
Jon Worthington almost won it for the visitors when his injury-time effort hit the post before Brandon was sent off for a heavy challenge on Rizzo in injury time.