Evenepoel was the only one who could go with the attritional pace of Pogacar, working as a set-up man for Del Toro, as the trio went to the line together, before the Belgian outsprinted the race leader to win.
He also moved into second behind the Slovenian after Vingegaard was forced to abandon the Tour. The Dane abandoned the race, crashing heavily in a tight roundabout, leaving the race with his arm in a sling.
Paul Seixas, the French teenager, was dropped by the trio, but limited his losses to just 58 seconds, meaning he lost the white jersey just 24 hours after gaining it. Del Toro, who took four bonus seconds for finishing third on the stage as well as time on the road, moved onto the podium behind teammate Pogacar and Evenepoel.
In the green jersey competition, Jasper Philipsen took another five points from Mads Pedersen's lead at the early intermediate sprint - a deja vu moment from stage 14. The Dane's lead is now 31 points going into Monday's rest day.
Pogacar still leads the King of the Mountains jersey. He is 22 points clear of Valentin Paret-Peintre, with Richard Carapaz six points further back.
Vingegaard crashes out
The big story, though, was the crash of Vingegaard. His team rode for much of the day, putting two riders in the breakaway to use as satellite riders.
They were controlling the peloton with 22 kilometres to go, heading down the gradual descent of the Cote du Mont when the road narrowed into a roundabout that included a lane divider.
The Dane, third wheel, slipped out on his own, crashing hard into the kerb. Teammate Sepp Kuss would go over the top of him, as Pogacar did well to avoid his eternal rival.
Jai Hindley and Del Toro would also go down, but it was Vingegaard who came out worse, leaving the Tour early in the back of a medical van with what was later confirmed to be a suspected fracture to his collarbone, which will require surgery.
Up front, a sizeable break looked to be within a chance of winning the stage heading up the final 11.3km climb. Quinn Simmons, Tom Pidcock and Adam Yates were the final three to be caught, with Lidl-Trek's Simmons the last to see the Pogacar train coming.
At that point, with five kilometres to go, Seixas was with a beleaguered Juan Ayuso as well as Evenepoel's teammate Florian Lipowitz. Ayuso would drop from the pair, given some help from Simmons, as Seixas ploughed on.
The 19-year-old, the big French hope to end their 41-year drought of Tour victory, is still within reach of the podium after a calculated display, but the day belonged to Evenepoel.
Remco proves doubters wrong
A fine time-trial rider, Evenepoel had never cracked a road stage at the Tour - until stage 15.
The Belgian phenom looked comfortable as he matched Pogacar, responding well to Del Toro's late attacks. As the trio headed into the final metres, he sprinted clear of the Slovenian to celebrate an emotional victory.
After Monday's rest day, attention turns to the 26.1km individual time trial on Tuesday, where Evenepoel will be sniffing another stage win.