Frenchman Julian Alaphilippe, whose Deceuninck-Quick Step team's acceleration in the crosswinds caused the decisive split, retained the overall leader's yellow jersey as he crossed the line at the same time as Van Aert.
It was the worst possible scenario for Pinot, one of the world's best climbers who was hoping to battle it out with Thomas in the mountains, as he lost a massive amount of time on the flat.
"Nothing to say, it was a shitty day," said a tearful Pinot, who started the day as the best-placed of the overall contenders after gaining almost half a minute with a brilliant attack in Saturday's eighth stage.