He leads Nibali by 44 seconds and Kruijswijk by 1:05 with one competitive stage left before Sunday's flat ride to Torino. Stage 20 is a 134-km mountain trek from Guillestre to Sant'Anna di Vinnadio on Saturday.
"Until now I was attacking, now I will defend," said Chaves. "I will leave my skin on the road."
Kruijswijk literally left skin on the road when he crashed in the rapid descent from the Colle dell'Agnello.
Kruijswijk started the 162km stage with a three-minute lead over Chaves but ploughed into a snow bank while descending the Colle dell'Agnello, the highest point of this year's Giro.
LottoNL-Jumbo's Kruijswijk, who needed to change bikes after crashing, was clearly struggling on the final climb and finished 4:54 behind Nibali.
Kruijswijk was not the only rider who fell victim to the Colle dell'Agnello on Friday. Minutes after his crash, footage emerged of Katusha's Ilnur Zakarin, who was fifth on the GC before the stage began, lying in a heap on the side of the road.
The Russian's race ended when he was taken to hospital with a suspected broken collarbone.
An emotional Nibali, the home favourite, burst into tears after his first Giro stage win of this year's race, which put him back into contention for a second title.
(Reporting by Simon Jennings in Bengaluru and Julien Pretot in Paris, editing by Ed Osmond)
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