The 26-year-old striker pounced from close range seven minutes from the end, after Eric Skora's cool finish had cancelled out Izale McLeod's opener for the Dons.
Dons' boss Danny Wilson made two changes to the team that beat Lincoln 2-1 in midweek, with on-loan duo Pablo Mills and Stephen Quinn returning after they were denied permission to play in the FA Cup first-round replay by their respective clubs.
Mills replaced the injured Mark Ricketts [knee] at centre-half, while Stephen Quinn replaced Nicky Rizzo on the left of midfield.
The Dons started brightly and McLeod converted the first chance of the match to put them ahead in the fifth minute. Trent McClenahan whipped a dangerous cross into the box and the 21-year-old striker stole in to send a diving header inside the far post from six yards for his eighth goal of the season.
The hosts continued to threaten with some neat passing football but Skora caught them on the counter-attack with Walsall's equaliser in the 13th minute.
Jorge Leitao was allowed to run the ball from his own half as Gareth Edds failed to close him down before slipping in Skora on the edge of the box, who rode McClenahan's tackle before firing underneath Dons' goalkeeper Matt Baker.
Matt Fryatt went close with a 20-yard strike that flew just over the angle as the visitors upped their game, before Dons' hopes were dealt a blow when danger man McLeod was forced off with a knee injury just after the half-hour mark.
Ian Roper came within a whisker of giving the Saddlers the lead four minutes after the break when his follow-up effort from close range was miraculously blocked on the line by Dons' keeper Baker.
Walsall skipper Chris Westwood's strike from Skora's corner was saved well by Baker, but the grounded keeper produced an even better stop to somehow keep out Roper's effort from six yards on the rebound.
And then Leitao found himself in the clear after Dean Lewington missed his tackle in the 64th minute, but the Saddlers' striker woefully fired straight at Baker from 12 yards as the Dons' defence appealed for offside.
But Milton Keynes fought back and Clive Platt's header from substitute Nicky Rizzo's cross was saved at full stretch by Walsall keeper Joe Murphy in the 76th minute, before Wilbraham won it for the Dons up with an instinctive finish in the 83rd minute.
Edds' fizzing 25-yard free-kick was spilled by Saddlers' keeper Murphy, and Wilbraham was there to slide home his third goal of the season from close range on the rebound.