Contador, who has worn the pink jersey since Wednesday's fifth stage but dislocated his shoulder in a crash on Thursday, leads Italy's Fabio Aru with Australian Richie Porte 22 seconds behind the Spaniard.
Movistar rider Intxausti crossed the line 20 seconds clear of compatriot Mikel Landa for the Astana team after a 15km category one climb to the finish, with Switzerland's Sebastien Reichenbach (Iam) third.
Intxausti was among 12 riders who broke clear from the peleton, after a wet and windy first hour spent jostling for position, and held off Landa's late charge.
The race favourites and top three in the overall classification crossed the line together, 35 seconds behind the stage winner.
"I'm really happy because yesterday and today were very hard," Contador told Eurosport.
"The pace was incredible today until the break finally went and then Astana made it difficult at the finish. I knew Aru would try to attack today. Richie and Fabio have come to the Giro to win. But despite my fall, I was able to respond."
Sunday's 10th stage is 215km from Benevento to San Giorgio del Sanno.
(Writing by Alan Baldwin in London, editing by...)
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