But despite his personal disappointment, he pledged his loyalty to his Team Sky buddy.
Thomas turned around to stare at the fan, but he admitted yesterday that he wasn't sure what had just happened.
MITCHELTON-Scott continue to throw punches at the Tour de France, this time animating Stage 18 with a daring breakaway attempt that came up short.
Peter Sagan, the three-time defending world champion and three-time stage victor in this year's race, crashed on the descent from the Col de Val Louron, the second mountain of the day.
Thomas will at least have the support of four-time victor Froome, who admitted he was now riding for his friend and team-mate after he lost time during Wednesday's 17th stage, falling to third.
Pictures on social media show a bearded man wearing an AG2R-La Mondiale shirt apparently reaching out to grab Thomas.
Meanwhile, Vincenzo Nibali will undergo surgery next week on the back he injured during a crash at the Tour as the Bahrain Merida cyclist aims to be back to ride in the Spanish Vuelta.
Team Sky described it as a misunderstanding and confirmed he was unhurt after having his arm grabbed.
Froome has said that he has been repeatedly spat at since the race started, and spectators have punched him and tried to make him fall off his bike.
A member of the Gendarme caused the two men to stop abruptly and crash before he then pulled Chris Froome off his bicycle.
After two grueling days in the Pyrenees, Thomas was able to enjoy his seventh day in the yellow jersey during the less challenging 106-mile leg from Trie-sur-Baise to Pau, which featured only two minor climbs and a flat finish.
Bahrain Merida doctor Emilio Magni said on Thursday: "The team and the rider agreed to the decision to have a percutaneous vertebroplasty surgery".
Stage 16 was briefly paused as riders, including Froome and Team Sky colleague, Geraint Thomas, were seen dousing their faces with water. Belgian star Philippe Gilbert lost control 60km earlier on another descent and flew spectacularly over a concrete wall and disppeared down a hill.
Although he was helped back onto his bike to finish the stage, won by French teammate Julian Alaphilippe, Gilbert emerged from the X-ray truck suffering from his endeavours.
With Froome conceding he has little chance of winning after falling further behind on Wednesday, that tension may ease a little.
But Dumoulin will feel he needs to take at least a minute off Thomas's advantage heading into the time trial, a discipline in which he is the reigning world champion.
"I think I am in a good position now", said Thomas.
'"G" has ridden such an fantastic race, he deserves to be in yellow and fingers crossed he holds it now until Paris. "I'm not going to change my mental approach and take it day by day, keep doing the small things right".