A day after the first rest day, the big guns were in no mood to take risks ahead of two more stages in the Alps.
Thomas has an overall one minute 25 second lead over Froome with Dumoulin third.
"He's won six grand tours, he knows how to ride a three-week race", Thomas told a news conference.
"I was feeling good, I really believed in my chances".
"You expect professional athletes to play sport and entertain without being touched or impacted on by the crowd, " Sky general manager Dave Brailsford said.
"Obviously Froomey is the leader".
'If people don't like Sky and want to boo that's fine, ' said Thomas.
This is the scenario 2012 Tour victor Sir Bradley Wiggins claimed would be a nightmare for his old team, but as questions about a leadership battle returned, the Welshman played the role of loyal lieutenant.Thomas said: "Froomey is the leader".
In the end, Van Avermaet produced a fantastic performance to finish 1min 43secs behind Alaphilippe, Thomas, Froome and Team Sky trailing over the finish over three minutes behind the stage victor. "My back hurts. I had trouble breathing and now I don't feel well standing", the Italian said after the stage. "Then it will depend on the situation and what's going on in the race". He wore the yellow jersey for four days previous year - before dropping to second behind Froome - then crashed out on a descent in Stage 9. "Legend gets used way too much but he's probably the best ever so I'm just going to enjoy this".
"I just followed Dumoulin and Bardet", said a dumbfounded Thomas.
During today's 12th stage of the Tour, Froome was accosted by a fan who lunged toward the cyclist as he made his way up a hill.
Kruijswijk continued to set an impressive pace and was all alone as he reached the top of the penultimate climb at Col de la Croix de Fer. But he was caught by Froome on the way up to Huez with 3.5 kilometres remaining. Stage 11 starts Wednesday and goes from Albertville to La Rosiere Space San Bernardo.