Ahead of stage 17, described as the most decisive stage in the final week, Thomas maintained his one minute 39 seconds lead on four-time champion and teammate Chris Froome.
Froome, notably, is expected to come under attack by Primoz Roglic as the Slovenian, in fourth 16secs behind him, targets a podium place in Paris.
Quick-Step veteran Gilbert was 57.2 km from the finish and in the lead of the 218km-long 16th stage when he negotiated a bend badly and flew headfirst over a wall.
With Thursday’s 170km 18th stage from Trie-sur-Baïse to Pau for the sprinters, Thomas’ next danger day after Friday is Saturday’s 31km stage 20 time-trial from Saint-Pée-sur-Nivelle to Espelette.
“It’s unfortunate Froomey lost time”.
“Thomas has been the strongest, and that’s the situation now”, Dumoulin said.
“Just try to think about what you are doing”, Portal said. I just felt my handlebars go as I was passing.
After the race had finished, Froome was caught by a police official and tackled down.
“I want to thank you for this”, Demare said. It was a day for the pure climbers. “We genuinely are good mates and honest and open”.
“But we have to keep on fighting”.
The last stage in the Pyrenees on Friday – the Tour’s so-called “queen stage” for its difficulty and drama – offers Dutch rider Tom Dumoulin his final real chance of capitalizing on any slip-up from Thomas.
Sky sporting director Nicolas Portal, a former rider with the team, appealed to fans to use common sense.
The 26-year-old Frenchman has spent the past days chasing points to add to his collection for the King of the Mountains’ polka dot jersey.
At the foot of that last effort, Quintana jumped away in impressive style followed by Martin who quickly found himself unable to sustain the pace of the twice Tour runner-up.
Safe in the knowledge Quintana was unlikely to claw back his overnight deficit of almost four minutes, Sky let the Colombian go.
“Egan himself decided, and it was the right thing to do, to stay with Froome”, said Portal. “(But) it just gave me confidence, that someone of his stature was struggling.
“I thought it was maybe an accident, just maybe an overly exuberant fan”, Thomas said.
Quintana, having benefited from the help of teammate Alejandro Valverde after he got into an earlier counter-attack, attacked solo with 6.4 km remaining.
Moments after cracking on the Col du Portet and slipping out of second place in the Tour, Froome’s afternoon got worse when, wearing a grey rain jacket over his jersey, he was mistaken for a fan trying to ride down the race route as he headed for the Team Sky bus.