"I think he's got nearly a two-minute lead on Dumoulin, which I think is a pretty comfortable lot", Froome told reporters after finishing 1:35 behind stage 17 victor Nairo Quintana and 48 seconds behind Thomas.
The defending champion came to France looking for a record-equalling fifth Tour crown and a rare Giro-Tour double, but after fading in the final two kilometres on Wednesday, Froome said he was all in for Thomas.
Tour de France director Christian Prudhomme condemned the actions of protesters who forced stage 16 of the race to be temporarily stopped as riders were caught in a cloud of pepper spray.
Chris Froome's chances of winning this year's Tour are now all but over.
"This was all I had, this was all we had today", Dumoulin continued. "I'm not here to make Froome lose the Tour, I'm here win it myself or do a podium".
Quintana had no such trouble despite two early stops due to mechanical issues, producing a brilliant long-range attack to secure a first Tour stage win since 2013 at the highest point of this year's race.
"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.More news: Over 1800 U.S. child migrants reunited
No danger then of this being a repeat of the uneasy relationship between Froome and Sir Bradley Wiggins during the latter's victory in the 2012 Tour. Yet when he arrived back at his team bus and responded to questions in French, he seemed dazed by the stage, a demeanour that was perhaps partly attributable to his collision with a policeman as he rode down from the finish.
"We feel safe. Obviously on some of the climbs not everyone's our fans but we don't feel threatened", Thomas said.
It happened about 18 miles (30km) into the 135-mile (218km) leg from Carcassonne to Bagneres De-Luchon.
The Netherlands' Tom Dumoulin remains third at 1:50, while Slovenia's Primož Roglič is fourth at 2:38.
But he lost the front wheel on a corner 6.5km from the end, and Alaphilippe zipped by in the polka dot jersey to collect his second stage win of the Tour.
The first test, surprisingly, on this stage 16 came after just 30 kilometres of racing.
"I didn't want him to have a bad day like he did but it just gave me confidence knowing someone of Froomey's stature was struggling, and I just knew I would be able to respond to the attacks". "[But] people should respect the riders and respect the race".