Three riders in Jurgen van de Walle, Jose Ivan Gutierrez (Caisse d'Epargne) and Julian El Fares (Cofidis) and broke clear on the 187.5km stage from Eperney to Montargis.
Their lead was six minutes at one stage but with 3.9km left, it was all over.
The sprint was now on with HTC Colombia doing the work for Mark Cavendish and David Millar working hard for the Garmin cause.
With less than 1km to go, the front men negotiated a tight left hand bend and with Mark Renshaw setting him up. Cavendish fought hard and crossed the line to win the stage.
Mark Cavendish
Gerald Ciloek was second with Team Sky's Edvald Boasson-Hagen third.
An emotional Cavendish spoke about his 55 road victory to his team's press office and said: "Yesterday [Wednesday] didn't go so great. I felt like I'd let the team down when I couldn't finish off with a win. "But the team has always believed in me. They gave it 100 percent for me today again, and they never gave up on me. I really wanted to win a stage in the best bike race in the world, too, and now I've been able to do that today. It's amazing."
"The pressure's been really intense," added Cavendish. "It's been really tough at times, but I want to thank all the people who have supported me though the hard moments. I've got an incredible group of friends and family, and a once-in-a-lifetime team, and they picked me up and all helped me to recover. We came here with ambitions to win stages, and I'll keep trying for more stages in the future."
Caisse D'Eparnge's Jose Ivan Guttierez won 2,000 euros for the Brandt Combatif rider of the day.
Fabian Cancellera keeps his yellow jersey with young jersey leader Geraint Thomas, who told ITV4 that British cycling was looking up, 23 seconds back.
Bradley Wiggins is 14th with David Millar 15th, Steve Cummings 67th, Jeremy Hunt 134th, Daniel Lloyd 152nd, Charles Weglius 174th,
Stage Six is a long one but one for the sprinters and is 227.5km long from Montargis to Geugnon.
Coverage can be seen live on British Eurosport at 1pm and ITV4 at 2.30pm.