Stanley had to endure plenty of pressure from the home side and survived several near misses before Molyneux pounced in the third minute of added time to move them five points clear of the relegation zone.
Wycombe made most of the early running and Accrington goalkeeper Paul Rachubka had to tip round a lobbed effort by Stuart Lewis after just eight minutes.
The Chairboys came desperately close early in the second half when Lewis placed a shot against a post after being put through by Matt McClure.
Rachubka was then called into action again when he pushed away Josh Scowen's low free-kick before Accrington's Amine Linganzi volleyed the ball wide after Will Hatfield's effort was deflected into his path.
And Stanley stole the three points deep into injury time when, after Craig Lindfield's corner was not cleared properly, Molyneux smashed the ball through a crowd and into the bottom corner.