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.
“Froomey is the leader. He’s won six grand tours,” said Thomas, who wears yellow for the second time after spending four days in the jersey at the start of last year’s Tour.
“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.
“For sure 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 he sped up again, passing the Mitchelton-Scott man inside the last 400 metres.
It gave Thomas the win after he was 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.
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.