Finishing just 17 seconds behind Tirreno-Adriatico race winner Simon Yates, Thomas displayed none of the pre-Tour poor form that resulted in his omission from the INEOS Grenadiers' Tour de France team.
The Welshman expressed his support of Bernal despite INEOS Grenadiers' Tour hopes crumbling as Bernal fell to pieces on the Colombier and slipped to over eight minutes and 13th on the general classification.
"It wasn't nice to see," Thomas said.
"Egan is a teammate but also a good friend. I've been through a lot with him. He helped me win the Tour and I was with him when he won his."
"We all know what it's like as athletes when you train for something and it doesn't quite go to plan. He obviously has a lot of pressure on him. He'll come back stronger. He's still so young and talented. He'll be back fighting for the overall again."
Thomas refused to take the bait when asked about his non-selection in the light of his strong Tirreno-Adriatico showing.
"For me, I'm just focused on the Giro," Thomas said. "That was the call we made and that's all I'm thinking about.
"Ifs and buts, you can spend all day questioning things.
"That's the call that was made and I'm really excited about the Giro now. That's my main goal."
Along with Chris Froome, Thomas finished well down the placings at Tour de l'Ain and Critérium du Dauphiné that prompted INEOS Grenadiers' management to boot the pair from their Tour de France team.
"Selecting the right leader in the right race with the right support team is critical," general manager Sir Dave Brailsford said in the official team announcement.
"We have had to analyse all the latest information to make sure we are in the best position possible to optimise our performances in the coming months."