Biarritz ran out 21-18 winners over Wilkinson's Toulon as the former England fly-half was left stranded in position for a last-minute drop-goal after his pack conceded a penalty.
And Harinordoquy, whose side qualify for the Heineken Cup after this victory, admitted that it was crucial to get the win after a tough season.
"Jonny Wilkinson has given a hard time to me in the past and he has done it to Dimitri as well - but it was Dimitri who gave Toulon a difficult time in this game," said Harinordoquy.
"This game changes everything for us - we have won a title and we will be in next season's Heineken Cup.
"It is probably now our best season from the last six years because before tonight we had not won anything in that time.
"It was the last game for Sylvain (Marconnet) and, to finish with a title, and I'm sure he - like all of us - will remember this night for a long, long time.
"We have had a lot of difficult games this season and they were useful exerience for this final.
And Yachvili concurred with his teammate, admitting that the early season struggles were now very much a thing of the past.
"We have lost two Heineken Cup finals, in 2006 and 2010. This is not the Heineken Cup but it is a title for us," he said.
"It has been a very hard season and that is why we are very happy. We never gave up. They tried to keep the ball for Jonny's drop goal but we defended very well.
"We deserved to win and It would have been very sad to lose two finals in the same season."