Contador came down on his left side just 55km into the second stage of the 2016 Tour from Saint-Lô to Cherbourg-en-Cotentin. Contador is already on the back foot after crashing heavily on the first stage, injuring his right shoulder. The cumulative impact of the two crashes meant he was unable to match the leaders' pace on the final climb: he came in 59 seconds behind stage winner, new race leader and teammate Peter Sagan.
Contador also lost 45 seconds to general classification rivals Chris Froome (Team Sky), Nairo Quintana (Movistar) and Vincenzo Nibali (Astana).
The Tinkoff rider admitted he was "not happy at all" after the stage.
"I lost more time than I had hoped to lose. I suffered another crash, I hit the handlebars and I was hurt on the other side from yesterday," he said. "This Tour has really started on the wrong footing."
Tinkoff directeur sportif Steven De Jongh added that today's crash was the catalyst for Contador's time loss.
"He couldn't stand up to climb and he blew his legs. That was the reason that he lost time.”
Contador has vowed to try and make up time in the mountains, but faces an uphill battle to take time out of climbers as strong as Froome and Quintana.
It may be some small comfort that Contador wasn't the only GC contender to lose time through bad luck. BMC's Richie Porte lost 1 min 45 sec when he punctured only 4.5km from the finish line.