Thomas would normally expect to be a domestique for four-time champion Froome at the Tour but victory at the Criterium against potential Tour contenders, coupled with the uncertainty surrounding Froome's adverse analytical finding from a drug test a year ago, means the Welshman could yet be riding for his own glory next month.
The Astana rider completed the route, which started in Frontenex, in a time of 3:34:11.
Thomas now holds an overall lead of one minute and 29 seconds in the general classification - with one stage remaining - ahead of England's Adam Yates (Mitchelton-Scott), who finished fifth on the day.
"I was always thinking of the next stage, the next climb and it's an incredible feeling [to win] and I think it will really start to sink in tonight". Now I realise I've won a massive race.
But it did give Thomas the chance to lead Team Sky.
And Yates' second place ensured the first ever British one-two in the race, with his second win on the WorldTour in 2018 confirming both he and the Welshman will head to the Tour de France in top form.
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He said it was learning from the previous days that helped him take victory on St Gervais Mont Blanc, delaying his attack to claim the stage win. "I managed to get a few more bonus seconds which is good".
"It was a hard stage, especially back to back with yesterday's, which was hard too".
It was Thomas' second World Tour stage race win after he won Paris-Nice in 2016.
Adam Yates was extremely happy to win the stage after a hard week of racing.
Thomas is next due to race in the National Road Race championships in Northumberland where he is down to do the time trial (29 June) and the road race (1 July).