The initial time checks showed that Nibali was losing a lot of time on the Dutch race leader, over 30 seconds in the first four kilometres, but he had his problems compounded by a rear derailleur malfunction in the final kilometres.
Nibali now sits at third overall at 2 minutes and 51 seconds behind Kruijswijk (Lotto NL-Jumbo) going into the final rest day.
He avoided reporters after the finish, going straight to the team bus before hopping on his bike and heading back down the mountain. Nibali later spoke to Cyclingnews sometime after the finish.
"It has been a bad day. I never found the right cadence, not counting the mechanical accident in the final."
The Italian champion looked stoic but concerned after crossing the line and will now have to take back a lot of time on Kruijswijk to win his fourth Grand Tour.
"Today I paid. Yesterday Valverde paid, maybe the day after tomorrow Kruijswijk could pay, I don't know. You have to accept results like that. There was a bit of irritation at the finish, but it's normal that after the race you have to catch your breath and it's hard to think about responding to questions straight away."
Astana were looking on the bright side after the finish, promising to fight on despite the setback.
"It can happen in a long three weeks race to have bad moments," said the team's sports director Paolo Slongo. "But we are calm, we know we have a good team and for sure we will battle in the last week."
Nibali was far from the only contender to lose significant time on the stage. Cannondale's general classification hope Rigoberto Uran lost three minutes and 18 seconds as well, slipping down to 12th overall and kissing his chance of a maiden Grand Tour win goodbye.