It was a day to forget for the former Tour de France winner who suffered a mid-race crash out of sight of the television cameras, and appeared in pain when he crossed the goal line.
The Visma-Lease a Bike leader managed to remount and chase back to the peloton after a visit to the medical car, but the incident clearly seemed to have taken a toll on him as he couldn't match the pace of the climbers in the end of the stage.
The young Frenchman Lenny Martinez won the stage ahead of Clément Champoussin (Astana) and Matteo Jorgenson (Visma), who were otherwise in the best position to take the stage from Saint-Just-en-Chevalet to La Côte-Saint-André.
Jorgenson thereby took over the yellow jersey from teammate Vingegaard, who is 22 seconds behind overall in second place.
Mathias Skjelmose (Lidl-Trek) also had a hard time on the last climb, even though he was considered favorite for the stage win after showing great form on Wednesday.
Skjelmose finished 28 seconds behind Martinez and dropped to sixth overall - 57 seconds behind Jorgenson in the standings.