Fernando Gaviria of Colombia and Dylan Groenewegen - who had each won two stages in this year's race - called it quits during Stage 12 to Alpe d'Huez.
It's unfortunate "Froomey" lost time. but yeah, I'm in a great position.
Greipel, one of several sprinters who pulled out in the Alps, while others, like Mark Cavendish and Marcel Kittel, missed the time cut, accused Demare of holding on to a vehicle to make it through the mountains on Stage 16.
Demare grinded his teeth though the mountain stages, narrowly avoiding missing the time cut on a couple of occasions.
Greipel, who also quit in Stage 12, later apologised on Twitter, saying he had relied on "incorrect" information.
The biggest threat to Thomas comes from Dumoulin, who said: "If I see an opportunity, I'll take it".
"It's very nice to win today, what can I say". (Cheating) is not my philosophy. "When I heard I had ten seconds lead or something, just 5km before the finish, I gave it all till the end".
Nibali broke the 10th vertebrae in a crash on the famous climb up to Alpe d'Huez last week when a fan caught their camera strap on his handlebars. Demare beat compatriot Christophe Laporte and Norway's Alexander Kristoff, who were second and third respectively as Thomas retained the overall leader's yellow jersey after 171 kilometres from Trie sur Baize.
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Thomas must navigate one more mountain stage Friday and a 19-mile time trial Saturday to ride into Paris on the final day Sunday in the yellow jersey. They include the iconic Col d'Aspin (12km at 7.3 per cent gradient), Col du Tourmalet (17.1km at 7.3 per cent) and Col d'Aubisque (16.6km at 4.9 per cent), the last of which is followed by a 20km descent to the finish.
"We're expecting the worst", admitted Thomas. Thomas praised the work of his team mates after they controlled the pace of the race all day, preventing most of their rivals from attacking as they set a high tempo in front of the main pack.
Having given a few interviews at the finish, Froome donned a large grey coat over his white Team Sky kit and descended the mountain accompanied by his bodyguard.
"Hopefully we won't have to use Froomey. It will be good to just keep doing what we've been doing".
Perhaps a bigger worry for Thomas and Froome concerns the unruly fans who have consistently affected this Tour by spitting at riders - or even reaching out to grab them.
Alaphilippe had earlier made it mathematically impossible for any rider to overtake him in the mountains classification when he also took all the points on the Col d'Aspin.
"I went through some hard moments in the first part of this Tour and lost some time", said Quintana, who is fifth overall. "I only saw him coming back on to the road".