The Belgian burst clear of the pack with around 400 metres left as they climbed to the finish at Vicenza in pouring rain after a 190 kilometre stage from Imola.
Contador was second, three seconds behind, as he led the peloton across the finish line.
After picking up six bonus seconds, the Spaniard extended his lead over Fabio Aru in the overall standings to 17 seconds.
Italian Aru came in at the back of the group after losing ground on his rival.
Franco Pellizotti attacked around 15 kilometres from the end and was joined by Tanel Kangert.
The pair opened up a gap of 24 seconds with only three kilometres left but, after Kangert broke clear, they were reeled in by the chasing pack.
Gilbert, 32, then sped away to claim the second Giro stage win of his career.
(Writing by Brian Homewood in Berne; editing by Toby Davis)
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