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"Victory is now impossible," said Contador after finishing the 200 km epic nearly four minutes behind determined Luxemburger Andy Schleck.
The Spaniard's unexpected slump means he is now seventh overall at 4min 44sec behind surprise race leader Thomas Voeckler of France.
Frank Schleck, Andy's older brother, is third overall at 1min 08sec behind Voeckler, with Australian Cadel Evans - now seen as the Schlecks' biggest rival for the yellow jersey - in fourth at 1:12.
Contador came into the race with question marks over his ability to perform in the crucial third week having competed in and won a gruelling Giro d'Italia for the second time in May.
But on Thursday it appeared that a knee injury he had suffered inside the first week following a series of crashes had flared up again.
Early on the first of three major climbs the Saxo Bank rider fell to the back of the main peloton, and he was later seen consulting with the race's official doctor.
Andy Schleck's Leopard-Trek team drove the pace hard all day, and they were sure to notice Contador was not on one of his best days.
Halfway up the 14.1 km Col d'Izoard, Schleck looked back and, noticing Contador was much further back in the peloton, went on the attack.
It went unchallanged, allowing Schleck to build a convincing lead over the main peloton which was boosted when he caught two of his Leopard-Trek team-mates that had got into an earlier breakaway to provide late support if needed.
Contador could only admit: "Andy played his cards well. He sent two of his guys in the breakaway, it was an intelligent move. You have to take your hat off to them."
As Schleck forged ahead to a prestigious stage win, and a possible maiden yellow jersey, Contador failed to produce any of the incisive attacks that have become his trademark during his past six Grand Tour successes.
The Spaniard even provided more unexpected drama when, inside the final km, he slid off the back of the small group of favourites being driven by Australian Cadel Evans.
Contador admitted his only thoughts then were about survival.
"In the last 10 km I was going through a really bad phase, but it was a difficult day from the start.
"When I got dropped all I could think about was trying to finish."
After the stage Contador was given medicine for his knee pain, which he hopes will abate by the third and final day in the mountains on Friday.
"I'm not used to the kind of situation I was in today. Now I have to get rest, recover and look ahead to tomorrow."
