Wilbraham bagged a hat-trick against Cheltenham on Saturday and followed that up with a superbly-taken strike in the 36th minute to ensure County remain five points from the play-off places.
Wilbraham saw a shot deflected over early on while Jason Puncheon shot straight at new Wales call-up Owain fon Williams after being released by Flavien Belson.
The visitors then grabbed a deserved lead as Puncheon released Wilbraham, who turned Jonny Mullins superbly before converting with aplomb from 16 yards.
Fon Williams twice denied Belson just before the break and Mullins thought he had levelled shortly after the restart but the goal was disallowed for a foul on Dons keeper Willy Gueret.
Stockport piled on the pressure late on, but the Dons held on to reinforce their promotion hopes.