Thomas rode in fourth at the top of the bad climb to the Planche des Belles Filles ski station in the woody Vosges mountains of eastern France.
"It was a decent day", Thomas said.
"The first day wasn't what I expected but now I'm back on top", said the Jumbo-Visma man on the finish line on the banks of the Soane river on a baking afternoon. Meanwhile, Ciccone goes down as the 269th yellow jersey in its 100-year history.
Team principal Sir Dave Brailsford had talked up the 22-year-old Bernal in the build-up to the Tour - declaring him "ready" to contend - but by Friday was happy to see Thomas hog the limelight. "I have no one to blame but myself, and I really hope that no one else got hurt because of me".
Ciccone took over the yellow jersey from Julian Alaphilippe, moving six seconds in front of the Frenchman overall, with Teuns now sitting third and New Zealand's George Bennett in fourth.
The Top American rider in the race, van Garderen was 36th overall, 10 minutes and 26 seconds behind race leader Giulio Ciccone. After my Giro, there were quite some teams interested but for me, it was pretty clear I wanted to stay with Trek-Segafredo, where I feel so at home.
"I think maybe everyone is getting a bit carried away with Egan", he said. It's one of those climbs where you have to be patient. Any normal bike rider would have gotten off long before and even some of the elite were pushed to their limit over the course of four brutal climbs - some as steep as a 24 per cent incline.
Stephane Rossetto and Yoann Offredo formed a leading duo for most part of the 230km flat stage.
Spending the day in the breakaway, Ciccone mopped up much of the mountains points on offer on the Tour's first hilly stage on 2019, but still sits in second in the climber's classification, 13 points behind Tim Wellens, Alaphilippe taking 11th position.
Pinot, who grew up 30 kilometres from the summit finish, was right on Thomas's tail, losing just a couple of seconds to the champion.
"I know that the terrain will suit him well and that six seconds is nothing", said Ciccone, nicknamed Il Gekko for his fast climbing abilities.