Slovak Peter Sagan reserved enough strength in the hills of the Alsace region to win a reduced bunch sprint for his 12th overall Tour de France stage win on Wednesday.
Since the Planche des Belles Filles featured for the first time on the Tour in 2012, the rider in yellow after that stage went on to win the race - Bradley Wiggins in 2012, Vincenzo Nibali in 2014 and Chris Froome in 2017.
Among the top contenders, Thomas is fifth, 49 seconds behind, and leads sixth-placed Bernal by four seconds and seventh-placed Pinot by nine.
"I think majority should be in a boxing ring rather than in a cycling race, yeah I guess that is sprinting", he said after losing his position and the opportunity to win his first Tour stage since 2017.
"Tomorrow is going to be a huge test, for me and everyone", said the 27-year-old former soldier.
"I try every day, and then one day you get it", said the burly Sagan. "I thought it would be a more solid day - it's never easy, but it was steady for the first three climbs", said Thomas, whose performance lifted some of the doubts about his condition after a crash forced him out of the Tour de Suisse last month.
The Slovakian also extended his lead in the points category, and now leads Australia's Michel Matthews by 47 points as he bids to win the green jersey for a record seventh time.
Sagan turned on the power from 150 meters out to beat pre-race favorites including Jumbo Visma's Wout van Aert, a breakout star of the race who came second while Italy's Matteo Trentin came third.
Fellow Briton Adam Yates lost 14 seconds to Thomas in the final moments of the stage but moved up to 14th place overall.
The 2019 Tour, with little time-trialling and mountains galore, should prove a climbers' dream.
Welshman Thomas looked relaxed after the race.