The English fly-half kicked what proved to be the winning points in Toulouse three minutes from time but there was still time for Morgan Parra to miss a penalty for Clermont with the last kick of the game.
To be fair to Parra the kick was from 50 yards out, and while he had the accuracy, the ball fell agonisingly short.
Toulon will now face defending champions Toulouse in the final at the Stade de France.
Clermont had started the match as favourites but despite having the bulk of possession could not score a try.
Instead it became a penalty battle – Wilkinson put Clermont 12-6 in front with two minutes to go but Parra kicked two penalties to level it.
However, Toulon got the better of the final exchanges to book their trip to Paris.