Pinot's FDJ team pulled in front at the foot of the Col d'Aspin, a 12km climb at an average gradient of 6.5 percent, but the Frenchman, third in the 2014 Tour and one of the outside favourites for Paris, was then dropped.
After the 162.5km from L'Isle-Jourdain, he finished six minutes and 41 seconds behind stage winner Steve Cummings (Dimension Data) and is now almost 10 minutes down on current overall leader Greg van Avermaet (BMC).
"After two kilometers I realized I was not at my best."
More importantly, he's lost touch with his key rivals for the overall classification, giving riders like defending champion Chris Froome (Sky) a three minute head start even before the most difficult phases of the Tour begin.
"I simply didn't have the legs. There's no excuse to look for," Pinot said.
"It's three times that I arrive in the Pyrenees and that I lose ground. That's it. I find myself with the same sensations as in the Dauphine. I'm not 100 per cent and in the Tour, you have to be 100 per cent.
"Of course, it's a waste. It's a season that almost goes to crumbs. The Tour is the highlight of the season and from the first mountain stage, the objective is over. It is not a matter of preparation.
"We looked to reach our peak for the Ventoux, but we're not machines. To program a peak it's more easily said than done. We'll see tomorrow. If it's like today, there won't be any surprise."