Andy Butler had equalised ten minutes from time after Sam Baldock opened for the home side.
The Terriers set up to frustrate in the first half and did a good job for the most part as the high-flying Dons had little joy in attack.
Their only real effort of the half came in a moment of magic when Dons' Jason Puncheon used an absolutely outrageous piece of skill to go round his marker and then made a menacing run to the edge of the box before rifling a shot against the stanchion.
The second half was played out more in the Terriers' half as the Dons upped the tempo.
15 minutes in Jude Stirling played a ball through the middle that was dummied by Aaron Wilbraham, Luke Chadwick ran onto the ball to go one-on-one with the 'keeper before feinting to shoot and instead just coolly squaring for Baldock who tapped home into the empty net.
It forced Town to up their game and Anthony Pilkington may have done better with a volley, before Booth then headed just wide from Pilkington's corner with 15 minutes to go.
They didn't rue the miss though as they then went one better
From Pilkington's corner Butler's header was deflected in past the despairing dive of Willy Gueret.
Dons could have still taken the points when substitute Ali Gerba was played through one-on-one with Smithies but his finish was well saved by the legs of the big 'keeper.
That wasn't the end of the action though as in added time Flynn hit both posts with an effort from the edge of the box that left everyone baffled after a lightning quick break.