The Chairboys were gifted the win by Bristol City loanee striker John Akinde's third goal in successive games just four minutes before half-time.
But Gills striker Simeon Jackson missed a penalty six minutes after the restart, after being felled by Dave McCracken in the box.
The home faithful were not happy, suggesting justice had been done when Jackson got up and fired high over Jamie Young's bar.
Wanderers started at a pace, hitting the post through Chris Zebroski's shot from outside the area in just the second minute.
Skipper McCracken saw a header deflected wide on six minutes, while Jackson had his first effort saved by Young moments later.
Although this was an entertaining contest, we had to wait at least another half hour for another golden opportunity, which also fell to Jackson 15 yards out in the 40th minute. He shot over.
He was made to pay a minute later when Akinde slotted home under Simon Royce from close range after a pinpoint through ball from Lee Sawyer.
Jackson then missed his penalty, the first meaningful action of the second half, before Curtis Weston missed the target for the Kent side in the 63rd minute.
Gillingham bossed the second half, as Andy Barcham's 12-yard effort was blocked by Tommy Doherty with 19 minutes remaining and a goalbound Jackson effort in the 83rd minute was blocked by Lewis Hunt with four minutes of normal time left.
But Wycombe managed to hold out for a vital win, especially seen as Brentford were held to draw at home by Exeter City.