The Colombian misjudged a corner on the descent of Alto del Moncayo, flipping over his bike as it broke apart in the barrier, causing injury to his left foot, knee and back.
He spent nearly two minutes on the ground before he remounted his bike, finishing the stage in 82nd, more than four minutes behind stage winner Tony Martin (Omega Pharma-QuickStep).
The Giro d'Italia champion now sits 11th overall, 3min 25sec behind new race leader Alberto Contador (Tinkoff-Saxo).
"I was feeling great in the uphill, but at that point of the descent my bike simply did not brake enough," said Quintana.
"Before the turn, I was tightening my shoe, which was a little bit loose, but I think that didn't have an effect on my crash. The thing is that I kept breaking for quite long, but it wasn't enough because the bike didn't stop, and I crashed.
"Fortunately, I could avoid having a bigger crash and I did not hurt myself really badly. I'm hurting my left ankle and I also have blows all over my body, but I hope it's nothing serious. This is cycling. I lost some time and I might be switching to help out Alejandro (Valverde) so we can conquer the overall podium."
Bittersweet day for Movistar
While it was a bad day for Quintana, his team-mate Valverde put in a strong time trial performance to finish 22 seconds behind Contador to move into second overall.
“I'm happy with myself. We're staying in second place, really close to Alberto, but it's a bittersweet taste with Nairo's crash," said Valverde.
"I didn't know anything, I was told when I finished. It's awful to have such a crash, when you're in the lead, clocking good times. Being the two of us closer in the overall would have been better for our interests, but the only important thing now is that Nairo is still racing. I'm sure he will recover well, even though I'm told it was quite a blow. We'll keep fighting to do great in this Vuelta.
"Losing so few seconds to Alberto and finishing before (Chris) Froome and Purito (Joaquim Rodriguez) is fantastic. I know tomorrow's finish: it's a demanding climb, really tough, and I just hope legs respond well. It seems like it's going to be good weather up there and I hope it plays on my favour."
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