An immaculate seven from seven penalties made it another miserable afternoon for an English club against Wilkinson in Europe, but it was his 73rd minute drop goal that had the crowd aghast as he created a nine point gap.
"It has been a great event and it was a good match for us. To come out on top against a team like Saracens is a big thing for us," said Wilkinson.
"Today was more about fighting hard to the last minute and hanging on in there. Fair play to Saracens, they are one of the top teams in the English Premiership and we saw that out there.
"We are pleased to be where we are but, with respect to Saracens, we have a lot of work to do. It's about having a fundamental base and working hard for each other.
"To be captain for the day at Twickenham was a great honour for me, but you are only as good as your last game. I'll have to get out on the training field and keep practising because you can't rest on your laurels, although, thankfully, we have a season that now continues.
"I have an immense amount of respect for Owen Farrell - he is fantastic for English rugby. For me, being on the sidelines and watching him and Toby Flood playing for England is great.
"He put in a huge hit on me when I dropped the goal. We had a few words on the floor and I apologised to him for being a bit lucky."
Clermont recently overtook Toulon at the top of the Top 14 and the two teams will now challenge each other for a league and cup double at the end of the season.
"Two French teams in the final in Dublin will be interesting. Clermont are a hell of a team and we know they are at the top of their game. It all means we have work to do," admitted Wilkinson.
"We've got to ask ourselves some serious questions and come back fighting for the final. We have still got a game to go before the final, but we will be excited about going to Dublin."