Accelerating 1km from the finish line, the 31-year-old outpaced Pierre Latour and Alejandro Valverde in the final sprint and claimed his second Tour de France victory after 5 years.
While they fought back to join the chase group, a third group led by Lotto and their rider Primoz Roglic struggled to stay in touch.
Behind him, Team Sky's Geraint Thomas took two seconds to move three seconds behind Greg Van Avermaet in general classification.
A group of five riders broke early on the 181km run from Brest to Mur-de-Bretagne and when the Quick Step team of stage contender Julian Alaphilippe suddenly accelerated on a plain, the peloton split into three with 100km remaining. "I said I needed some time, and I didn't feel good in the first stages".
"I'm glad I made the legs do the talking today.
It makes this Tour de France a success for us already, and anything else is a bonus".
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Tintin and Asterix have always been rivals in the world of the comic strips for both are popular for their entertainment and art. But Southgate revealed he could not listen to it for many years.
Belgian Greg van Avermaet has retained the leader's yellow jersey.
Dutch rider Dylan Groenewegen won the stage ahead of Fernando Gaviria, who like Sagan has also won two stages in this year's Tour.
"I'd like to thank Greg (Van Avermaet) because he did me a favour when he went for it, I don't know if he did it on goal but he dropped a lot of people", said Sagan, who has tightened his grip on the points classification's green jersey.
Groenewegen grew up in a cycling environment as his grandfather was a bike manufacturer and his boyhood coach was Jean-Paul van Poppel, victor of nine sprint finishes at the Tour de France. "People said I was not good enough after the first sprints but that's not true", he said.
This was the fourth sprint stage of this year's Tour, and the fourth in which Cavendish failed to feature, rolling home to a 10th place which is his best of the race so far.
Friday's 231-kilometer seventh stage will take the cyclists from Fougeres to Chartes.
Martin was one of several team leaders along with former Tour victor Vincenzo Nibali and two-time runner-up Nairo Quintana who were caught off-guard by an attack by Quick-Step midway through the stage during a straightaway that was exposed to crosswinds.