A late flurry saw him claim third on the day, nine seconds behind Yates, and third overall but Thomas crossed the line ten seconds later to earn the second UCI WorldTour stage race win of his career after Paris-Nice 2016.
"I was always thinking of the next stage, the next climb and it's an wonderful feeling [to win] and I think it will really start to sink in tonight".
Team Sky's Thomas came home 21 seconds behind Spain's Bilbao (Astana), who staged a heroic solo effort 12 kilometres from the finish to triumph.
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 previous year, means the Welshman could yet be riding for his own glory next month.
The attacks has been pulled back during a fast start. This shot from race organiser ASO shows what it is like out on the road
It came on a 110 kilometres stage from Frontenex which is nearly a carbon copy of this year's Tour de France stage 11.
"I made a good recovery though and I'm in good shape, ready for the next training block ahead of the Tour".
Froome has asthma and received permission from cycling chiefs to use legal asthma drug salbutamol at the Vuelta.
"It's been a learning process starting in a new team so getting this win for UAE is great", he said.
"Hopefully the authorities can just get their act together and have a decision, but I've got 100 per cent faith in him". He is in the a year ago of his current Team Sky contract and wants his long-term future resolved before the Tour de France starts. Now I realise I've won a massive race. The guys rode really well for me. I get to ride the races I want and I am a leader in a lot of them. Pierre Rolland (FRA) Team EF Education First - +41 Drapac p/b Cannondale Overall leaders 1.
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