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The 35-year-old got up and running with a successfully converted eighth-minute penalty, but just four minutes later Castres hit back through Max Evans, who found a way through for the game's only try.
Wilkinson added his side's second successful penalty of the night moments later, yet once more the current holders replied, this time through Rory Kockott's penalty.
A pattern was beginning to emerge in the contest when Wilkinson cut the gap to one point when he found the sticks with another penalty, and it got even better for the former England international when his drop-goal put Toulon ahead shortly before the interval.
Wilkinson added his fourth penalty on 53 minutes to put his side into a fairly commanding position, before Delon Armitage edged Toulon even closer to the title with his angled kick seven minutes from time.
Castres looked to respond, but they were unable to make any further damage to the scoreline as Toulon held out for the famous victory.