The striker just poked over the line to give the Dons their first win of the season despite protests from the visitors.
It could have been a very different result had Adebayo Akinfenwa brought his finishing boots with him as the big striker missed a glorious chance in second-half injury time.
Just 15 miles separates the two towns but at times the game lacked the spark of a real derby and Dons ran out deserved winners with a dominant second-half display.
The first half did have the feel of a real derby to it and both teams played some committed and attacking football.
The first decent opportunity to fell to the home side after a good passing move ended with Dean Lewington crossing an inviting ball in the box. Wilbraham beat Chris Doig to the ball but couldn't head past Mark Bunn who made a decent save.
Minutes later, Mark Wright might have done better as he blazed over from 20-yards.
The Cobblers got more dangerous as the half went on and had the best chance on the half-hour mark.
Calamitous defending let Akinfenwa clean through on goal but, with all the time in the world, the big striker fluffed his left-footed shot wide.
He the robbed the ball from Danny Swailes and unleashed a decent shot from 25 yards that Willy Gueret pushed wide.
The Dons started to impose themselves in the second half and controlled possession.
The created their first chance after a fluid and patient passing move ended with the ball finding Wright on the wing. He beat his man and sent an accurate cross to the back post for Florian Sturm, who somehow headed wide from close range.
Thankfully the woeful Austrian was taken off soon afterwards and his replacement, Shaun Cummings, looked more dangerous within seconds of being on as he hit a snapshot just over.
And the deadlock was broken soon after in controversial fashion.
Wilbraham scrambled Peter Leven's corner over the line at the back post from close range despite the efforts of Danny Jackman on the line who claimed to have cleared.