The 31-year-old won the stage by five seconds from Stefan Küng (BMC Racing) with Sky team leader Chris Froome sixth, 13 seconds back.
Asked whether the team would change anything after the result, sports director Servais Knaven said "No, we have a plan and in the plan Geraint is already one of our key riders.
"It's not like we were putting him in as an early helper. We have our plans with him and this only shows that we made the right decision to put him in the role we put him in."
With the first summit finish coming on stage five to La Planche des Belle Filles, Thomas is expected to stay in yellow for the next few days.
Watch: Tour de France stage one highlights
However Knaven stressed that the team were at the Tour primarily to try and guide Froome to a fourth yellow jersey, and that nothing would be allowed to compromise this.
"The main goal is to win the Tour with Chris," he continued. "If someone has to work one day and lose his own chances that's what has to happen.
"But we'll see. Maybe it can work out that some guys don't have to work too hard and can still do a decent GC, but that's not the main goal.
"The main goal is to have the yellow jersey with Chris in Paris and all the other things are a nice bonus. Like this! This is a super nice bonus but that's not what we came for. We came for the yellow jersey in Paris."
He fought on for a couple of days, posting an impressive second place behind eventual overall winner Tom Dumoulin (Team Sunweb) in the stage 10 time trial, before abandoning ahead of stage 13.
The Welshman was apparently in some of the best form of his life heading into the race, and Knaven said the team would still try to keep him in a good position so long as that didn't damage Froome's chances.
"He’s pretty versatile and we will maybe use him on different occasions, in the medium mountains, in the high mountains.
"Hopefully we can keep him in a good position until we come in the Alps and then we will see how things go and where we are and what tactically we have to do."
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