Quintana led the race going into Tuesday's 10th stage time trial, but lost time after going over his handlebars while trying to adjust his pedal clips on a descent.
And though the Colombian survived that crash, another incident on Wednesday's 11th stage saw him go out of the race with a suspected broken collarbone.
The crash took place in the peloton just 20km into the 153km stage from Pamplona to Navarre, and the Giro d'Italia winner was taken directly to hospital for checks, thereby ending his race.
A large group reportedly went down, with a media motorbike apparently involved in the chaos.
BMC Racing Team’s Steve Morabito has also been forced out of the race.
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