Groenewegen would double his tally at the race, as the Team LottoNL-Jumbo rider crossed the line first in 4 hours, 23min and 36sec.
The Tour de France arrived at the foot of the Alps after the long transfer from Roubaix yet continued dishing the dirt, on and off the road.
"This win was fantastic for my self confidence, I feel under less pressure now, a sprinter needs confidence", he said, "I'll be trying to win again tomorrow now!"
After nine stages, Thomas lies second overall heading into today's 10th stage from Annecy to Le Grand Bornand, 47 seconds behind BMC's Greg van Avermaet.
Thank you for signing up for the 5 Things to Know Newsletter.
Groenewegen followed up Friday's success in Chartres with a Bastille Day win in Amiens.
Sen. Rand Paul Shrugs At Russian Election Interference: 'We All Do It'
Trump leaned forward in his chair, his hands tented in front of him and frequently glanced over at the Russian president. Protesters have been on the streets of Helsinki to denounce the policies of both Trump and Putin.
That meant that Sagan officially finished second, with John Degenkolb in third.
"It is very emotional, I went through such a hard period so today is pure happiness", said Degenkolb, who suffered several fractures and a serious finger injury after he and some team mates were hit by a vehicle during a training ride in January 2016. "I saw Gaviria and Greipel were fighting for position but I saw the finish line and thought, 'This is the moment'". "I had no legs to beat the first two guys".
Froome attacked as soon as Bardet punctured for the last time just at the end of the last cobbled sector, but the Frenchman, who at some points was lagging 40 seconds behind, benefited from huge pulls by his team mates Tony Gallopin and Oliver Naesen.
"No one could have imagined this is the way Stage 9 would have started but we still have 7 riders in the race and we are behind them 100% of the way". The riders passed kilometer 231.
Another strong performance came from UAE Team Emirates rider Dan Martin, battered from his crash yesterday, but who even managed to pick up a late bonus second today.