Barguil was slow to get up after the fall but eventually finished the stage atop Croix de Chaubouret. The Dutch team is not yet certain if he will start Friday's stage, according to a statement on the Giant-Alpecin website.
"Hopefully Warren will feel alright to continue tomorrow, but he'll have some more checks this evening to make sure there’s no damage done," said Giant-Alpecin coach Christian Guiberteau.
The team was well positioned near the front of the thinned-down peloton after the day’s penultimate climb, with John Degenkolb, Koen de Kort and Georg Preidler helping to keep Barguil and Tom Dumoulin in position and out of trouble. But as the road turned upward, a touch of wheels caused Barguil, who finished eighth overall in the Vuelta a España last year, to fall along with several other riders.
"The guys did a good job throughout the stage today and both John and Koen made it over the second-to-last ascent to be able to help Georg, Warren and Tom ahead of the last one," Guiberteau said. “It was good to see five guys still there this late on.
"We were a bit worried that Warren wasn’t going to be able to get back on the bike but eventually he was OK to continue and finish the stage, which was good to see. I am pleased to see Tom coming around again and his chances of a good result overall are still good."
Dumoulin, who was fighting sickness before the race started, finished 15th on the stage, ceding just over a minute to stage winner Richie Porte (Sky) and 56 seconds to overall race leader Michal Kwiatkowski. He's now the team's best-placed GC rider in 15th, 1:13 down.
"Today was either going to go better than expected or not well," Dumoulin said after the stage. "So I’m pretty pleased with the outcome. I felt good on the final climb but was still lacking a bit of power and didn’t have the shape for a top 10 and to follow when the last attacks came.
"I’ve tried to take it as easy as possible in the past few days to recover a bit," Dumoulin said. "Now I hope that I can continue to improve and have a good final weekend."