Sagan, who won his third consecutive road race championship past year, rode to victory in Sunday's flatter second stage.
BMC captain Porte is 56sec off the lead, Adam Yates 1min 05sec, defending champion Chris Froome at 1min 06sec, with Thursday's stage winer Dan Martin at 1min 30.
His deficit to yellow grew to one minute 42 seconds as Greg Van Avermaet finished second to Degenkolb on the day, two parts of a trio 27 seconds ahead of Froome's group. I thought when I first kicked I was floating, I was quite excited.
"There's no reason I can't look at it [the Mûr de Bretagne], even though I'm contending for GC [the general classification]", Martin said earlier this week.
"The fact he wasn't in the sprint was good for me", Sagan, who now leads Gaviria by 33 points, said.
"I was following quite good wheels but it was choppy".
Gaviria and green jersey holder Sagan, who have won two stages each in this year's race, ended up following Groenewegen home in a line without ever looking likely to challenge him, with Arnaud Demare in fourth.
Belgian Greg Van Avermaet retained the leader's yellow jersey ahead of Saturday's eighth stage and said he hope to go to the mountains with it next week after what he described as a relaxing day.
Bardet was already trailing Froome, and after losing 28 seconds is now 1:45 off the leader's pace after he broke his back wheel and had to change bikes with Tony Gallopin.
Fernando Gaviria and Peter Sagan have dominated the sprints so far, and there's no reason to bet against them here.
In the 2015 tour, he finished second on the same route as today's stage.
All the top contenders for the overall victory enjoyed a comfortable day as the race heads towards a much-feared ninth stage featuring cobbled sectors on Sunday just before the first rest day.
Team Sky's Geraint Thomas remains in second place, with Van Avermaet's team-mate Tejay Van Garderen in third, now eight seconds back.
"I was a bit nervous because of the headwind, I didn't think it was going to happen", Martin, 31, said. "The Tour is very long and we are only on the fifth stage".
The peloton set off amid good racing conditions for the longest stage on the race, with a finish line opposite the 800-year-old cathedral of Chartres, a UNESCO world heritage site.