Ahead of stage 17 on Wednesday, described as the most decisive stage in the final week, Welshman Thomas maintained his 1min 39sec lead on four-time champion and team-mate Chris Froome.
Starting the 17th stage with a deficit of 1min 39sec to Thomas, the Kenyan-born Briton showed rare glimpses of weakness on his way to finishing almost a minute behind his Welsh teammate at the final mountaintop finish of the race at Saint-Lary-Soulan won by Colombian rival Nairo Quintana of Movistar.
Froome had put a raincoat over his racing uniform to keep warm, on a day when he cracked on the final climb to Col du Portet, drastically decreasing his chances of a record-tying fifth title.
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This year's Tour has also been marked by protests against Team Sky, which includes defending champion Chris Froome.
Froome has also been pushed and spat at by spectators in what has been a hostile response from the French public towards Team Sky.
The Tour de France - cycling's most prestigious race - was temporarily halted Tuesday after tear gas, used to disperse protesters by police, inadvertently got into the eyes of some riders.
While Froome was dropped in the finale, at one stage it looked like going the other way as he covered a move by LottoNL-Jumbo's Roglic while Thomas hung back on the wheel of Dumoulin, leaving the Dutchman to close the gap. "But it's fantastic. I'm really happy".
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"We just got to look after [Thomas] now", Froome said.
Frenchman Pierre Latour, who wears the white jersey for the best young rider, said he noticed police were using tear gas when he arrived at the road blockade. I'm not sure they'd have liked their football players being spat at in Russian Federation (at the World Cup).
"Froomey said on the radio maybe with four or five km to go that he wasn't feeling super and that gave me confidence", Thomas said. I've won the last three Grand Tours I've done now. Tomorrow will be a very special race and I would like to do a good race in front of the many Basque fans I will find on the road.
Yates led Alaphilippe by 20 seconds at the top of the Col du Portillon climb 10 kilometres from the finish but lost control with 6K to go, falling to the pavement on a left turn and sliding across the road.
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"It's the first time I've ridden for GC (general classification)".