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Team Sky all-rounder Thomas finished an impressive sixth on the 191.5km race opener from Passage du Gois to Mont des Alouettes at only six seconds behind unstoppable Belgian Philippe Gilbert.
As Omega-Pharma's Gilbert pulled on the coveted yellow jersey, Thomas was the best placed of the riders aged 25 and under, finishing two places ahead of Estonian Rein Taaramae of Cofidis.
The Welshman, who with the rest of his team are supporting Bradley Wiggins' bid for a place on the podium in Paris, admitted he did not expect to step on to the post-stage podium so soon.
"I went in today just wanting to look after Bradley and hopefully get Edvald (Boasson Hagen) up there," said Thomas.
"I could get used to it. It's always nice wearing this. A nice surprise as well because I hadn't really thought about it to be honest. I thought maybe after the team time-trial, if it went really well."
At the team time-trial on Sunday, Gilbert risks losing the yellow jersey to the teams who possess several time-trial specialists, such as Sky, HTC-Highroad, Garmin and RadioShack.
Although Thomas finished the top Sky rider, Wiggins also finished just 06sec behind Gilbert.
Either rider could realistically take the yellow jersey from the Belgian on Sunday if their British outfit win Sunday's 23km team race against the clock.
In the team time-trial, official times are taken from the fifth rider over the finish line. For Wiggins to pull on the yellow jersey ahead of Thomas, the Englishman would have to finish one second ahead of the Welshman.
Team manager Dave Brailsford said: "He (Thomas) could be, but so could Bradley.
"But for Geraint it's a good way to start the Tour de France."
