There were further signs of the ill-feeling towards Team Sky and Froome in the finale, with several fans booing and gesturing towards the Sky riders, while Froome had what appeared to be a clear liquid thrown at him.
The profile of Friday's 13th stage could help the Italian, a former two-time victor of the Giro d'Italia, if he decides to continue. Watch every minute live on Eurosport Player, plus minute-by-minute live blog and extensive video highlights - breakaways, sprints, stage finishes, interviews, incidents; you won't miss a thing. I'm climbing slightly better here.
He said: "Honestly I'm speechless".
"I don't actually recall it but I'm not surprised, we've had a bit of that and it's always been water from what I've seen", Thomas told a news conference. I was fully in the zone then fighting for position. "I just can not believe it". I hope that doesn't happen.
Saturday's Stage 14 is a hilly 188-kilometre trek from Saint-Paul-Trois-Chateaux to Mende as the race makes its way to the Pyrenees Mountains.
Froome and Dumoulin both competed at the Giro d'Italia in May, finishing first and second respectively.
Although Dumoulin failed to drop his Team Sky rivals, he was able to put them under pressure with a strong attack before the race reached the summit of the final ascent. "Froome closed the gap and attacked, and it was Thomas again who closed the gap to Froome".
After overzealous fans marred Thomas' win on Thursday atop the Alpe d'Huez, the otherwise complete calm of Friday's leg was briefly disturbed by a man on the roadside who tossed a smoke bomb into the centre of the peloton as it passed by with 16 kilometres left.
Now he insists that he is not just racing for another podium spot in a grand tour, even if it would be his highest finish ever in the Tour. Plus, the intimidating strength Team Sky showed through the Alps threatened to shut down the race. "He showed that in Tirreno-Adriatico, where he also attacked on a steep climb". No chance in hell did I think I was going to win this.