The Colombian posted a photograph of himself on Instagram giving the thumbs up in hospital after receiving treatment for his injuries.
Betancur went into the stage as the Movistar team's highest-placed rider overall in 16th spot.
The 27-year-old was riding in a select group that included race leader Chris Froome (Team Sky) and Alberto Contador (Trek-Segafredo) when he was brought down in a crash with American Tejay van Garderen (BMC Racing).
Van Garderen appeared to fall first on the descent of the Alto del Garbí, leaving Betancur with no room for manoeuvre. The BMC rider later said that it was a 'mystery' as to what had caused the incident.
Betancur fell heavily, but despite his injuries he managed to get back on his bike and finish the stage, 12 minutes and 31 seconds down on winner Tomasz Marczynski (Lotto-Soudal).
He was taken to University Hospital of Sagunto, where the Movistar team says he underwent a CT scan and X-rays. The tests showed that he had fractured a bone in his right ankle, which required a plaster cast and therefore it is impossible for him to continue in the race.
Watch: Vuelta a España 2017 stage six highlights
Betancur was subsequently moved to La Fe hospital in Valencia to have surgery on his facial injuries.
This year's Vuelta was the first time since 2014 that Betancur has ridden in the race, and he looked set to post his best-ever result in the Spanish three-week race after placing 18th overall in the Tour de France.
"A pity to have to say goodbye after returning this way, but we will return with more strength!" he said on Instagram.
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