Outplayed for 60 minutes and seemingly out of the game after Clermont scored two tries in five blistering second-half minutes, big-spending Toulon stunned their rivals with a Delon Armitage try and a conversion by Wilkinson, playing in his first European final.
Ten years after kicking England to World Cup glory, Wilkinson collected the trophy at the Aviva Stadium following the conclusion of Toulon's second Heineken Cup campaign.
"Those guys are the best. They were dubbed mercenaries when they arrived here. They were never mercenaries," coach Bernard Laporte said in a television interview of his starting 15, just four of whom were Frenchmen.
Armitage over moon with silverware
All the drama was saved for the second half and a tentative start to the game came as no surprise, given three points separated the teams in their two domestic clashes this year.
Clermont scrum-half Morgan Parra exchanged penalties with Wilkinson in the first 12 minutes.
A tight game seemed to suit Toulon and the trusty boot of Wilkinson, with Clermont's backline needing 20 minutes to spark into life.
Clermont, semi-finalists last year, went close to the Toulon try line three times before the half hour but on each occasion they were penalised.
The television match official was called into action again two minutes after the break when Napolioni Nalaga, knocked off balance as he brushed past one tackle, danced down the touchline and was adjudged to have dived over in the corner for the opening try.
Parra failed to convert and was punished within minutes by another penalty from Wilkinson.
The reprieve was short-lived when Clermont made it two tries in five minutes. Aurelien Rougerie was the architect, snatching a dink over the top from Brock James before giving the Australian the ball back to dive over under the posts.
Wilkinson trimmed the deficit to six points with a penalty on the hour and Toulon somehow found themselves in the lead minutes later when Clermont were made to pay for allowing the game to turn sloppy.
A simple turnover from Juan Martin Fernandez Lobbe sent fullback Armitage clean through, jeering James as he sped past.
Wilkinson then added the conversion to give Toulon the lead for the first time.
It left Clermont, who have been among the strongest teams in Europe in recent seasons and went into the game with a 100 percent record, heartbroken once again.
"It hurts but I prefer to think that we came within a point of something great. We'll have to work harder and come back stronger," said captain Rougerie.
Clermont reflect on final defeat