Jan Polanc (UAE Team Emirates) fired free from an early escape and soloed over the black lava fields to win the fourth stage.
Russian Ilnur Zakarin (Katusha-Alpecin) slipped away from the favourites’ group and Thomas won the sprint for third behind. The bonus seconds moved him to second overall at six seconds behind pink jersey Bob Jungels (Quick-Step Floors).
"Everyone was just watching everyone, no one really went," Thomas said.
He arrived at the bus after an anti-doping check and spoke surrounded by Italy's fans.
"Obviously it was a bit of headwind the last 2K and I think everyone was a bit apprehensive. I felt good and it was nice to win the sprint for third and get a couple of seconds. Not a bad day."
The 17.95km Sicilian climb opened up near the top with lava fields spreading toward the finish line and volcano's mouth. The wind, chilly but warmed by the island's sun, held most back.
Vincenzo Nibali (Bahrain-Merida), a two-time Giro winner, tired under three kilometres. Zakarin's move stuck at 1.1km.
"I felt good on the climb, but like myself, I think everyone didn't want to go too early, too deep. I think everyone is finding their legs and sussing each other out," Thomas continued.
"Nibali did try, but with the wind it's always tough. Guys still had a few team-mates and they rode at the front. If it was a bit more of a select group it might've been different.
"When Zakarin went everyone looked at each other, but when Nibali went, obviously everyone is going to chase straight away."
The Welshman, who is co-leading this Giro with Sky's Mikel Landa, sits second and Englishman Adam Yates (Orica-Scott) holds third ahead of a group at 10 seconds. Most of the big stars are in that group including Nibali, Nairo Quintana (Movistar), Tom Dumoulin (Sunweb) Thibaut Pinot (FDJ) and American Tejay van Garderen (BMC Racing).
Thomas seems in perfect spot. Had he taken the pink jersey, Sky would need to work early for its leader.
"I guess [I am in the perfect spot], but I wouldn't turn down the pink jersey, it'd be nice to wear that. But it's a good start,” continued Thomas.
"Obviously it's a nice psychological boost to win the sprint but at the end of the day, it's still a hell of a long way to go to Milano. I think will know a lot more from Sunday [with Blockhaus, the next summit finish].
"Blockhaus will be bigger test on Sunday. It's a lot harder climb and we'll see where everyone's really at there."
Tomorrow, the race heads towards Messina where the sprinters should have their chance. In the evening, the Corsa Rosa makes the small ferry ride over to Italy’s mainland.
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