Thomas attacked with six kilometres left of the 108.5km stage from Albertville to take his second career Tour stage win and with it the overall lead of the race, one minute 25 seconds ahead of Froome.
This is the scenario 2012 Tour winner 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. He’s won six grand tours.
“It’s just how I feel. Some guys might sit here and give some PR bull**** but I just say how it is with me and that’s how it is. Froomey is the leader.
“I’m not going to sit up and lose time, but I think we’re in a great position. It’s just a bit of an unknown for me to race over three weeks. It’s the ideal scenario at the moment and long may it continue.”
It might prove tough for Thomas to sacrifice himself in the service of Froome from this position, but the 32-year-old said he would follow team orders.
“It depends on the situation and what’s going on in the race” he said. “How the team want to ride. If I have to pull towards the end then I will. We’ll see.”
When Thomas first attacked his mission was to catch Tom Dumoulin, who peeled off the peloton on a descent leading to the final climb up to La Rosiere. Thomas did that comfortably and, when Mikel Nieve slid into view, trying to win the stage from the breakaway, another prize was on offer and Thomas sped up again, passing the Mitchelton-Scott man inside the last 400 metres.
It gave him the win after he had been second on an almost identical stage of the Criterium du Dauphine in June, en route to overall victory in the race.
While Thomas was riding to victory, there was the fascinating sight of Froome staying behind to cover counter-attacks from Romain Bardet and Nairo Quintana.
With that job done, Froome latched on to a move from Irishman Dan Martin, eventually catching Dumoulin to finish third on the stage, 20 seconds back.
“It’s an amazing position for us,” Froome said. “I don’t think we quite expected that going into today’s stage. I think everyone probably expected Alpe d’Huez to be the more decisive stage, and it might very well still be, but it puts us in a fantastic position.
“(Thomas’ attack) was a bit of a spur of the moment thing for us but it made sense, it was perfect, we didn’t even have to talk. I let the wheel go because I knew the onus would be on the rest of the guys to chase.”
But while Team Sky could celebrate, Team Dimension Data did not get the Mandela Day gift they were hoping for as Mark Cavendish was eliminated from the Tour for missing the time cut. The 30-time stage winner was dropped early on and spent the entire stage off the back, but rejected a ride in the broom wagon before crossing the line 65 minutes after Thomas.
Cavendish was in trouble long before the explosive end to this short mountainous stage, which was designed to promote attacks.
The battle for yellow was on once BMC’s Greg Van Avermaet was, as expected, dropped midway through, with Movistar’s Alejandro Valverde launching a long-range attack on the Col du Pre almost immediately after.
Team Sunweb’s Dumoulin bridged over to the Spaniard on the descent off the Cormet de Roseland before leaving him behind on the climb to the finish, while Sky kept their powder dry until the finale.
The fast finale caught out several, with Mitchelton-Scott’s Adam Yates shipping almost five minutes and dropping to 16th overall, perhaps leaving the Lancastrian to focus on stage wins.
Dumoulin is up to third, one minute 44 seconds behind Thomas, with 2014 winner Vincenzo Nibali of Bahrain Merida fourth, two minutes 14 seconds down.
Martin’s late moves, encouraging after a bruising stage nine to Roubaix, saw the UAE Team Emirates rider move up to 10th, level on time with Movistar’s Quintana, three minutes 16 seconds down.