The LottoNL-Jumbo rider, who finished third in stage four on Tuesday, timed his sprint perfectly in the last metres of the uphill finale and crossed the finish line ahead of compatriot Giovanni Visconti and Portugal's Jose Goncalves.
"The finish was a bit different to yesterday," Battaglin, who previously won Giro stages in 2013 and 2014, said. "Yesterday was really a powerful sprint on a really steep climb.
"Today was a steep climb but at two kilometres to go, and I had a little bit of time to rest and recover and do a really good sprint."
Australian Rohan Dennis managed to weather the storm to hold on to the pink jersey in Sicily ahead of Thursday's mountain stage to Mount Etna.
The BMC Racing rider retained his one-second lead over defending champion Tom Dumoulin, with four-time Tour de France winner Chris Froome 55 seconds back in 19th place.
"It was a nice day on the bike, on quite a slow pace because of the head wind," said Dennis.
"I felt a bit of stress every now and then but I am glad to be in the Maglia Rosa. We're only on day five, that means 16 days to go. Tomorrow will be another story with the Etna. I'm looking forward to see how I'll go up there."
Astana rider Miguel Angel Lopez was the only overall contender to suffer a setback after he crashed into a field with six kilometres to go, shedding 42 seconds on his rivals.
(Reporting by Hardik Vyas in Bengaluru; Editing by Toby Davis)
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