The 32-year-old finished the first mountain-top finish of the 2015 Tour in 11th position on Monday - two minutes, 51 seconds behind overall leader Chris Froome (Team Sky).
As Froome surged to his first stage win of the race, finishing 59secs ahead of team-mate Richie Porte, he built a 4:04 gap on Contador.
Prior to the season, Contador (Tinkoff-Saxo) announced he would attempt to win both the Giro and the Tour - a feat last achieved by Marco Pantani in 1998.
Contador- a two time winner of Le Tour- appeared fatigued as he struggled to push the pedals and crossed the finish line in an uncharacteristic stupor, refusing to speak to a host of reporters.
"It was hard to breathe," he revealed at the Tinkoff-Saxo team bus later.
"I didn't feel good.
"I struggled to breathe and couldn't spin my legs.
"I actually felt better in the saddle, which is the opposite of my best riding style.
"It was a bad day for me. I tried to do it the best I could but I was worried about losing even more time."
Contador is adamant he will bounce back despite the poor result and praised Froome on his stage victory.
"We've got to congratulate Froome. He's three points better than the rest of us," the 32-year-old said.
"He has done what he wanted and has shaken up the general classification."