Geraint Thomas finished in the select lead group of 20 riders that finished eight seconds down on lone stage winner Julian Alaphilippe, while Richard Carapaz was slightly distanced in the line of riders and lost five seconds to Thomas and many of his overall rivals.
Tao Geoghegan Hart and Richie Porte made it back to the peloton after the first crash sparked by a roadside fan holding a sign but were caught up in the second pile-up inside the final 10 kilometres and were unable to get back to the front of the race.
Porte lost 2:16, with Geoghegan Hart finishing 5:33 down in a bigger chase group.
Ineos Grenadiers started the Tour de France with Thomas, Carapaz, Geoghegan Hart and Porte all protected riders due to their previous Grand Tour success or recent superb form. However, that strategy will now surely change, with Geoghegan Hart and Porte likely switching to a support role.
"Happy to get through it but gutted about Richie and Tao," Thomas said as he warmed down post-stage.
"It was a solid day, stressful with a few crashes. In the big crash at the end, I had no idea who was in it. It ended up with Richie being in it which wasn't great. I was just concentrating on staying on my bike, basically."
Carapaz was happy to limit his losses on the final climb. "It was a very fast stage, and this last ascent was very explosive," the Ecuadorian climber said.
"The important thing is that G and I were up there and we'll continue onwards from here."
Thomas was not happy with his positioning before the climb to the finish but dug deep and stayed with the like of Tadej Pogacar (UAE Team Emirates) and Promiz Roglic (Jumbo-Visma) and puncheurs like Wout van Aert and Mathieu van der Poel.
"I was too far back on that last climb. At the time I thought 'it's OK, I'll sit here and then slowly move up when it lulls'. But it never lulled!" Thomas said of the constant speed and fighting for position on the climb.
"I think it was because Alaphilippe went so hard for so long, it was just full gas all the way up. It made my life a bit harder.
"For me personally it's not too bad. I never feel 100 per cent on the first stage after a few easy days."
Thank you for signing up to Cycling News. You will receive a verification email shortly.
There was a problem. Please refresh the page and try again.