Banned from racing by organisers - a decision welcomed in France - Froome was allowed to race after the UCI dropped its case against him.
Thomas, Froome, and the rest of the overall contenders slowly rolled across the finish line at Carcassonne and its medieval city walls 13 minutes after stage victor Magnus Cort Nielsen of Denmark.
Stage 11 last week, a 108.5-kilometer leg from Albertville to the La Rosiere ski resort, saw elite riders such as Alejandro Valverde attack from far out, forcing Team Sky to increase its pace far earlier than it would have liked.
"It's not a nice situation, and obviously we would prefer everyone to love us, but I'm not sure it's anything we've done, or especially that I've done, to deserve it", he said.
Froome was more evasive when asked if he would attack Thomas if in a position to do so.
Yet his Grand Tour ambitions have often fell short.
Although Lotto-Jumbo pair Primoz Roglic and Steven Kruiswijk have had ineffective stabs at Sky over the past week, Dumoulin is their biggest threat. The final margins will be determined in Saturday's time trial, but the rolling 31km course is an intriguing one given it may temper the advantages of the pure time trialists. He holds all three Grand Tour titles after following his fourth Tour win previous year with victory in La Vuelta and the Giro d'Italia, and has his sights set on a rare Giro-Tour double.
"I was lucky that it did not affect me too much, I had a bit of tingling in the back of the throat but I used some water to wash it out", said Thomas on the finish line in the spa town of Bagneres-de-Luchon, after keeping his overall lead intact.
Punching Other Cyclists Will Get You Kicked Off The Tour De France [Video]
"The last week is a battle of nerves for everyone". "I'm sure there would have been a word or two about that, but it's okay to spit at us and our staff?"
Thomas and Froome will now enjoy Monday's rest day before the intriguing intra-team battle for yellow resumes on Tuesday, with three tough days in the Pyrenees having the potential to be decisive. Such conduct is, unfortunately, unlikely to endear Team Sky to the home crowds when the relationship is already strained.
For Landa, only a concerted effort from fellow riders with the shared goal of reaching the podium in Paris will work.
Although Sky will be hoping to keep powder dry for the crucial third week, Froome said their rivals could try to steal time on the steep, 3km-long climb to the finish in Mende.
"Dumoulin and Roglic should collaborate and help".
"Thomas is on the verge of achieving a feat that cyclists dream of, to win the Tour".
At the 100th Tour in 2013, Froome proved why he deserved leadership status. Riders had to slow down when they reached the scene and footage shows them rubbing their eyes after passing through the demonstration.