The 27-year-old Colombian, sitting inside the GC top 20 at the start of the day, hit the deck when BMC's Tejay van Garderen crashed just in front of him on the descent from the final climb of stage 6.
He remounted and made his way to the finish just under five minutes down on the stage winner, but sustained serious injuries in the fall.
According to the Movistar team, post-stage examinations ruled out various head or hip concerns, but revealed an ankle fracture. Furthermore, the crash left Betancur with facial wounds that will require surgery.
With Betancur out of the Vuelta, Movistar no longer count any of their riders among the top 20 of their home Grand Tour, with Nelson Oliveira their best-placed rider at 24th, 2:45 back on race leader Chris Froome (Sky).