Groenewegen (Jumbo-Visma) powered through the wind ahead of Bahrain-Merida's Ivan Garcia and Philippe Gilbert (Deceuninck-QuickStep) to retain the yellow jersey and extend his overall lead to 12 seconds ahead of Michal Kwiatkowski (Sky).
“Today was a very tough stage because of the crosswinds," Groenewegen said. "There was a continuous fight for positions and a continuous racing at the limit.
It was far from easy. The team did a perfect job and after the last corner, they put me in an ideal position.
"It was a matter of waiting and to not start the sprint too early. When Trentin accelerated, I started my sprint and I was able to finish it off.
"Two stages, two victories: I am very happy. Tomorrow there is another flat stage. It will be a tough one again due to the wind, but we are going for it again.”
Simon Yates’s (Mitchelton-Scott) hopes of winning the race were dashed when he was among the casualties on a day of brutal crosswinds which repeatedly split the peloton on the 165.5km stage from Les Breviaires to Bellegarde - the 2018 Vuelta a España champion lost almost seven minutes.
They were only 23 riders left — including overall contenders Romain Bardet (AG2R), Nairo Quintana (Movistar) and Bob Jungels (Deceuninck-QuickStep) in the front group some 30kms from the finish line.
A late split meant only seven riders contested the final sprint.
BIG NAMES FORCED OUT
A crash after 59kms took Gorka Izagirre (Astana) out, as well as Warren Barguil (Arkéa Samsic), who was taken to a hospital for a scan after losing consciousness and later diagnosed with a fractured vertebra.
It is unclear how long Barguil will be sidelined but Arkea-Samsic general manager Emmanuel Hubert told local media Barguil's injury "is very annoying but he will recover soon and he will be very fine."
Izagirre injured his elbow where no fractures were found but a contusion of the left elbow and left hip was diagnosed.
Rigoberto Uran (EF Education First) was also among the casualties, fracturing his left clavicle and forced to abandon.
The Colombian went down on his left side in the middle of a pack of riders midway through the stage, and he was immediately taken for evaluation at a nearby medical facility.
“I had a tough crash,” Uran said after leaving the hospital. “Today, there was a lot of wind. I touched a rider, another rider touched my wheel. I feel disappointed, of course. I had good legs. That’s cycling."
Dimension Data also suffered some losses with a struggling Mark Cavendish not up to the pace in only his third race back from illness and GC contender Louis Meintjes out after a crash on a roundabout.
Meintjes returned to the race but lost too much time and would have missed the time cut.
“The racing was on and I went through a roundabout and I guess I misjudged it a bit. It’s pretty painful and I lost a bit of skin," Meintjes said.