The Slovakian three-time world champion blasted ahead of his final rival, Italian Sonny Colbrelli (Bahrain Merida) in the last metres to win the uphill stage five kick at Quimper. It marked his second stage win and gave him more points to his green jersey lead.
"My team-mates did a fantastic job to keep me in front," Sagan said.
"Greg Van Avermaet launched the sprint too soon, and in fact, it was a help for me and [Sonny] Colbrelli. Thanks Greg!
"I spoke with Colbrelli during the stage, I told him not to surprise me. He said, 'come on Peter, at least give me one, but I told him that I already have so many second places at the Tour that I don't want another."
Sagan won five consecutive green points jerseys in the Tour de France through 2016, but famously in 2015 he racked up five second places and two third places without a victory.
Last year, the jury disqualified him for bumping with Mark Cavendish in the sprint of stage four. He went home with one sprint win.
He is back and in charge in 2018, having already won stage two and taken the yellow jersey for a day and on Wednesday, won stage five – a technical and Classics style stage.
"Peter is a super strong rider," race leader Greg Van Avermaet (BMC Racing) said.
"To drop him, you have to win the team time trial. I don't know what happened there for him.
"It's hard to get rid of him, he's a strong climber, sprinter... everything. I always tried to beat him, I can sometimes, but it doesn't happen that much any more."
The two often face off in the Classics and in the Tour at times too. Van Avermaet has the jersey, but Sagan has two wins so far.
Colbrelli placed second to Sagan on day two and again on day five. Sagan would not gift anything because he is unsure how strong he is in this 2018 Tour de France.
"I don't know if I'm at my best," said Sagan. "The other day I had bad moments in the team time trial. I hope to improve."
Bora-Hansgrohe controlled the race with Quick-Step and BMC Racing before Sky took over in the final tricky kilometres.
"Today everything went well and I also had luck. My companions did an amazing job, Bodnar in the final covered me and brought in the best position.
"On the final kick, Sky pulled full gas, Philippe Gilbert has tried to attack from afar and Van Avermaet went too soon, but we calculated the right time. Winning at the Tour is always a nice feeling.
"And Sonny? If you try day after day, a win will come."
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