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Froome's reign in Grand Tours appeared to waver when he first slipped behind six kilometres from the end of stage 16. He then lost contact for good with around three kilometres to race while Welshman Thomas rode away with his rivals in the yellow jersey.
"It was a very intense day but I've got no regrets," Froome said after finishing nearly a minute down on his team-mate. "G has ridden such an amazing race and he deserves to be in yellow – and, fingers crossed, he holds it now until Paris.
"That's professional cycling. That's what a team is all about. I'm happy just to be in this position. I've won the last three Grand Tours I've done now, so it's certainly been tough build-up for me but I'm still going to try and fight for the podium and try to keep G up there in yellow."
Nairo Quintana (Movistar) won the 65km stage ahead of Dan Martin (UAE-Team Emirates), while Thomas took the bonus seconds offered for third place on the stage. He now leads the race with 1-59 over Tom Dumoulin (Team Sunweb) and 2-31 over Froome.
Froome lost 48 seconds on the climb and fell from second to third overall as Dumoulin moved ahead. The race comes on the heels of his 2017 Tour de France and Vuelta a España wins and his 2018 Giro d'Italia title in May.
"I just didn't have the legs in the final," Froome explained. "Like I've said, I've won the last three Grand Tours now and G has ridden an absolutely faultless race this year so he fully deserves to be in the yellow jersey and fingers crossed he finishes it off and gets the job done to Paris."
Paris is on the horizon, but three more days remain before then: a sprinters' stage to Pau, a mountain stage with a downhill finish to Laruns and the time trial in Espelette.
"I think he's got almost. What is it? A two-minute lead on Dumoulin? Which is, I think, a pretty comfortable buffer," Froome said.
"He looks really strong so I imagine he'll be able to finish it off. We've just got to try and look after him now, these next few days."
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