Second-half goals from Pawel Abbott and Wagstaff cancelled out Luke Chadwick's early opener and handed the Addicks their second victory over the Dons in eight days.
Chadwick gave the Dons a dream start when he collected Lewis Guy's pass and slotted the ball past Rob Elliot from 10 yards in only the second minute.
Chances were few and far between thereafter but Abbott sparked the game into life when he equalised eight minutes into the second half, powering a close-range header past David Martin from Kyel Reid's pin-point cross.
Martin produced a good reflex save to prevent an own goal by Dons defender Mathias Doumbe, who then twice went close with powerful headers from set-pieces.
But Wagstaff won it for the Addicks five minutes from the end when he stole in unmarked at the far post to volley in another cross from Reid.