Wilkinson produced a faultless kicking display at the Stade Felix Mayol as he landed five penalties and a conversion before succumbing to an elbow injury five minutes after half time.
Tries from Sebastien Tillous Borde, Benjamin Lapeyre and former London Irish flanker Steffon Armitage ensured Quins were unable to repeat December's famous Heineken Cup triumph at Toulouse and set up a semi-final showdown with Stade Francais at The Stoop.
Toulon started brightly against a Quins side missing England skipper Chris Robshaw and star fly-half Nick Evans through injury, with Wilkinson striking as early as the fourth minute before hitting the target again in the eighth to hand the home side a 6-0 advantage.
Wilkinson continued to steal the show with a further three beautifully struck kicks putting Toulon way out in front before the half hour.
The first came from the 15-metre line on the right of the pitch and fully 45 metres out to re-establish the six-point gap at 9-3 on 13 minutes. The second arrived four minutes later as Quins were penalised for offside just five metres in from the right-hand touchline, while the third was from two metres inside the Quins half when Karl Dickson crept too far around the side of a scrum with 29 minutes gone.
Things got worse for Quins just three minutes later as Tillous Borde crossed for the game's opening try. Giant centre Mathieu Bastareaud supplied the incisive burst, with his forward pack driving him onwards before the scrum-half burrowed through underneath the posts from the resulting ruck.
Wilkinson added the straightforward extras to leave Toulon with a 22-3 lead at half-time but Quins began the second period in a far more encouraging fashion than the first and they twice came close to scoring inside the opening four minutes.
Mike Brown was brought down just two metres short moments after the restart before Quins fell foul of the TMO two minutes later. Prop Mark Lambert powered towards the line as Quins looked to reduce the gap but TV replays showed he had been held up by more than one Toulon defender.
Quins' task got even harder on 49 minutes when James Johnston was yellow carded for punching following the break up of a scrum just inside his own half and Australian playmaker Matt Giteau effectively put the game beyond them when he slotted a penalty after 51 minutes.
Toulon then added a second try seven minutes later as full back Lapeyre sliced through from close range after Giteau had switched direction and blindside flanker Pierrick Gunther had produced a wonderful offload.
Giteau knocked over the simple conversion to make it 32-3 with still more than a quarter of the game remaining and man-of-the-match Armitage picked up the try his impressive showing deserved when he drove over from a lineout deep in Quins territory with seven minutes left to play.
Danny Care claimed a late consolation after slipping through two tackles having taken a quick tap penalty on 77 minutes but it was far too little too late for Quins.