Italy's Sonny Colbrelli (Bahrain-Merida) took the stage victory, just ahead of Germany's John Degenkolb, in a reduced bunch sprint. Arnaud Demare (FDJ) finished in third place to retain the yellow jersey.
"It's the greatest victory of my career," Colbrelli said.
"It's incredible. I managed a perfect sprint and to beat riders like Degenkolb or even (Marcel) Kittel just shows that."
With six stages remaining, Porte is now in 35th place, 15 minutes behind Demare.
"It's not my kind of racing but I don't want to make excuses as to why I dropped," Porte said.
"I think we can learn more from a day like that than we do winning. It was a tough day for everyone, the whole peloton. No one is more disappointed than me, but I think I can repay my team mates later in the week with the time trial and other stages by going for the win there."
After the wind and rain of Monday, the peloton makes its way towards Chalon-sur-Saone on Tuesday.
(Reporting by Martyn Herman, editing by Neil Robinson)
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