Spain's Luis Leon Sanchez (Astana) took second place, 12 seconds off the pace.
Tinkoff-Saxo leader Contador, bidding to become the first man to achieve a Giro/Tour de France double since 1998, now leads Aru by 2:28 after the Astana rider finished 29th, more than three minutes behind Kiryienka.
"The result is a big surprise for me. I gave it all I had, and paced myself carefully all the way. I now lead Aru by a good margin, especially after the fall yesterday, but I have to keep a clear head," said Contador.
"The Giro is still long. Today has been a good day for us, and now we’ll take it day by day."
Costa Rica's Andrey Amador is third overall, 3:36 adrift of Contador ahead of a mountainous final eight days starting with Sunday's 15th stage, a 165-km trek leading up to Madonna Di Campiglio.
Australian Richie Porte, who was considered Contador's main rival before the Giro started, dropped out of contention after losing another four minutes to Contador.
(Writing by Julien Pretot in Paris; Editing by Toby Davis)
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