Bahrain Merida later confirmed that Nibali was out of the Tour de France after he had been escorted by police to Grenoble hospital for scans.
"The scan has confirmed what we feared," Bahrain-Merida team doctor Emilio Magni told Italian site Tuttobiciweb. "There's a fracture of the T10 vertebra. It's a non-displaced fracture but it's clear Vincenzo can't ride his bike again for at least 15 days."
"We don't know what Vincenzo will do tomorrow, we've got to speak all the staff and then decide. One thing is sure: now he needs some rest. In a few days well probably do another scan."
A video posted to Twitter of the crash appeared to show some sort of strap catch Nibali's handlebars as he rode past the crowd.
Speaking after the stage, even Nibali was unsure entirely what had happened in the incident that saw him hit the deck at pace.
"Bardet was in front with 10 seconds of an advantage and there were motorbikes between him and our group," said Nibali. ""The road became narrower and there were no barriers. There were two police motorbikes. When Froome accelerated, I followed him, I was feeling good. Then we slowed down and I hit the ground."
Nibali had an x-ray done at the finish-line, with the results inconclusive and requiring further information.
Nibali was whisked away to Grenoble hospital for further scans on his back. Immediately after the stage, Nibali gave his own appraisal of how he felt after the incident.
"I took a blow and I was a bit winded too when I tried to get up and go again," said Nibali. "Right now, I don't feel very well able to move on my feet. I hope it isn't something more serious, but we'll see in the coming hours."
Nibali himself looked in really good form, with the former Tour winner attacking earlier on the stage and reinforced by the fact that he was able to get back on the bike and nearly rejoin the leaders after the fall.
"Well, I was going well, I really believed in it," said Nibali. My legs were turning well, I had good sensations," said Nibali. "The first attack I made was only to see if someone would respond, but my idea was to make the real attack in the finale."
The injury comes as a double blow, with Nibali also losing time on the stage after finishing 13 seconds back on the stage. He was asked if he believed he should be treated as a similar situation to the scenario in 2016 where Froome, Porte and Mollema all collided with a moto late in the stage to Mont Ventoux and were awarded the same time on the finish.
"I don't know because Froome was in the yellow jersey and that was a bit different," Nibali said. "These are things that can happen because there are lots of people and fans on the roadside, and the road narrowed."
It turned out no to be of consequence for the Italian as he pulled out of the race entirely after the news from the medical staff.
The incident with Nibali was far from the only one on the typically rowdy Alpe d'Huez stage, with Romain Bardet (AG2R La Mondiale), Steven Kruijswijk (LottoNL-Jumbo) and Chris Froome (Team Sky) all experiencing difficulties on the final climb.