Froome minimised the damage to his chances of a first Vuelta win by fighting back to finish 20sec adrift of the main group of general classification favourites, including Nibali.
“It’s never nice to crash like that, but I’m just grateful that I’m not injured and everything is good to go tomorrow,” Froome told Spanish TV station Teledeporte.
Poland’s Tomasz Marczynski won his second stage of the race as he took the 160.1km ride from Motril to Antequera in a time of 3hr 56min 45sec from Spanish duo Omar Fraile and Jose Joaquin Rojas.
Marczynski cashed in as an early 14-rider breakaway was allowed to fight out the stage win.
“It’s incredible, it’s my dream since I was a kid to win one stage on a big tour alone and today the dream became real,” said Marczynski.
Back in the pack, Froome looked perfectly set to maintain his lead until disaster struck just over six kilometres from the finish.
The four-time Tour de France champion was forced to change bike due to a mechanical problem and then hit the floor seconds later as he tried to get back up to speed.
Froome’s Sky teammates Mikel Nieve and Wout Poels helped him limit the damage, but he couldn’t bridge the gap back to the Nibali group.
“It’s never nice to lose time, but I have a fantastic team around me. I had two teammates with me all the way to the end,” added Froome. “The Vuelta is not over yet and there are a lot of big days ahead. The race is not over until we reach Madrid. I just need to be at my best every day now.”
Alberto Contador was the big winner on the day as the three-time Vuelta winner gained 42sec on Froome after breaking away from the rest of the chasing group to move up to ninth overall.
However, Contador remains 3min 13sec back on Froome overall.
Nibali finished 22sec behind Contador alongside the rest of the riders in the top 10 bar Froome.
Colombia’s Esteban Chaves remains third overall, but is now just 2min 13sec down on Froome.
Today’s largely flat 13th stage takes the riders 198.4km from Coin to Tomares.
Stage 12 results
1. Tomasz Marczynski (Lotto) 3:56:45”
2. Omar Fraile (Dimension Data) +52”
3. Jose Joaquin Rojas (Movistar)
4. Pawel Poljanski (BORA)
5. Stef Clement (LottoNL-Jumbo)
6. Brendan Canty (Cannondale) +1:42”
7. Anthony Perez (Cofidis) +2:50”
8. Jan Polanc (Emirates)
9. Andreas Schillinger (BORA)
10. David Arroyo (Caja Rural) +3:00”
Overall classification
1. Chris Froome (Sky) 49:22:53”
2. Vincenzo Nibali (Merida) +59”
3. Esteban Chaves (Orica-Scott) +2:13”
4. David De La Cruz (Quick-Step) +2:16”
5. Wilco Kelderman (Sunweb) +2:17”
6. Ilnur Zakarin (Katusha) +2:18”
7. Fabio Aru (Astana) +2:37”
8. Michael Woods (Cannondale) +2:41”
9. Alberto Contador (Trek) +3:13”
10. Miguel Angel Lopez (Astana) +3:51”
