Burton went a man down in the 20th minute as Marcus Holness was given a straight red by referee Mick Russell for raising his hands in the direction of AFC Wimbledon midfielder Sammy Moore.
However, despite being a man down it was Burton who edged ahead after half an hour as Alex MacDonald's low corner found its way to Adam McGurk whose left-foot shot took a deflection before finding the back of the net via the post.
The hosts pushed for a leveller before the break but failed to make their pressure count with Luke Moore heading over and Harry Pell forcing Jordan Pickford in to a smart save with a powerful drive from distance.
Wimbledon continued where they left off after the break and they were deservedly level in the 55th minute as substitute Chris Arthur's over hit cross found fellow sub George Porter, whose cut back was slotted home right footed by Michael Smith.
And the comeback was complete in the 69th minute as Pickford fumbled Arthur's cross and Jack Midson tapped home from close range.
The points were made safe five minutes later as Andy Frampton powered home a header following a Moore corner.