With the scores level at 29 apiece and extra time looming on the Cote D'Azur, Wilkinson slipped back into the pocket and ended Stade's hopes of a maiden European trophy, reminding Cheika of the agony of that defeat to Quins in the process.
"I'm sad for the team because we deserved more, a lot more, just like in last year's final," said Cheika, after his men led 16-3, 19-11 and 26-23 at the Stade Felix Mayol.
"It was like a replay of last year's final against Harlequins, with the same result."
Cheika, who led Leinster to their first Heineken Cup crown in 2009, was full of praise for his players after they ran Toulon far closer than many expected despite making a number of changes to their starting XV.
The visitors outscored their illustrious hosts by two tries to one and worked their way back into a game that appeared to be slipping away from them after 15 unanswered points from the boot of Wilkinson at the end of the first half and the beginning of the second.
"I can't doubt the spirit of my players," added Cheika.
"It's easy for people to criticise Stade Français but my team is full of heart and they showed their value against a side which is made with millions of euros.
"We came here with a lot of changes - we had a back row in the centre (George Smith) - and I think the spirit shown by this Stade Français side meant we deserved the victory. We feel we deserve to be in the final."