Toulon, who had not been French champions since 1992, won the Heineken Cup last weekend and on Saturday took their revenge for their defeat in the final against Castres last year.
It was meant to be all about Wilkinson, with 'merci Jonny' stitched into all the Toulon team shirts, and it was all about him in a packed Stade de France, with the black and red army occupying the south end of the stadium and the PA playing God save the Queen at the end.
"I would like the thank the whole team, the crowd but also Castres and all the other teams in the Top 14. I don't have the words, can't thank the French public enough," Wilkinson said.
"Thank you for all the memories. I have spent more than half my life with a rugby ball, it's going to be a big change."
Wilkinson scored four penalties and a drop goal while Delon Armitage sealed it with eight minutes left.
Castres's points came from Rory Kockott's boot and a try from Max Evans.
A Wilkinson penalty put Toulon ahead, only for the defending champions to open a 7-3 lead when Evans scored an 80-metre try after following up his own kick.
Kockott added the extras but Toulon had Wilkinson, who added two penalties and a 23-metre drop goal to put his side just ahead at halftime.
Toulon opened a five-point lead early in the second half when Wilkinson curled a fine penalty between the posts from a tight angle.
With eight minutes left, another penalty for Toulon on the left side of the pitch was left to Armitage, who duly delivered to put his side beyond reach.
Wilkinson, 34, made his test debut in 1998 at the age of 18, becoming England's second-youngest international, with his second test a 76-0 thrashing at the hands of Australia in the so-called "Tour of Hell".
From that inauspicious start he went on to play 91 test matches for his country, despite suffering a number of serious injuries, helping them to the 2003 World Cup title and runners-up four years later.
He played six tests for the British and Irish Lions, and is the second-highest test points scorer behind New Zealand's Dan Carter with 1246.
Noted for his unique kicking stance that was later replicated by players around the world, he was deadly in front of the posts and unflappable in the most highly-charged of match situations, never more so than the 2003 World Cup final against Australia in Sydney.
While he did not like to be defined by his drop goal in the last minute of extra-time that won England their first and only world championship, it is undoubtedly the image that comes to mind for rugby fans the world over.