The virtual race is being held on the popular Zwift training platform after the COVID-19 pandemic forced the postponement of the actual annual July race until the end of August.
The final stage had the riders competing over six laps in a simulated Champs-Elysees and Clarke edged out Team Ineos' Filippo Ganna and Ryan Gibbons of NTT Pro Cycling to win the stage in 51 minutes 44 seconds.
"Last week I went too early in the sprint and I figured out how early I went and made sure this week I timed it right," Clarke said. "It was still hard to pass everyone, I came from a long way back."
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NTT Pro Cycling topped the general classification with 500 points followed by Rally Cycling in second (267) and Trek-Segafredo in third (232).
Lauren Stephens clinches final stage of virtual Tour de France
In the women's race, Lauren Stephens of TIBCO-Silicon Valley Bank used a powerup to beat Drops' April Tacey and Twenty20's Georgia Simmerling in the final sprint.
"Winning the yellow jersey as a team and the final stage was more than we expected coming into first women's Virtual Tour de France," Stephens said.
"We came into the stage today focused on taking the green jersey because we knew we were going to keep the yellow jersey. We knew a hard, controlled race was best for our team and that's what we did today."
Will Clarke wins final stage on virtual Champs Elysees
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