The reigning Giro d'Italia champion went down hard onto his shoulder 22 kilometres from the finish on stage 15 - a 183.9-kilometre day from Champagnole to the summit finish of Plateau de Solaison.
The Danish star slid out during the descent of the Cote du Mont as the road narrowed through a roundabout. Visma Lease-a-bike teammate Sepp Kuss could not avoid him as he crashed into Vingegaard, with Isaac del Toro and Jai Hindley also going down on the same corner.
The trio all got on their bikes as Vingegaard remained on the ground before being attended to by the Tour's medical team. He left the race with his arm in a sling in the back of an ambulance.
Vingegaard, before the crash, was second in the general classification, four minutes and 30 seconds behind race leader Tadej Pogacar.
On Saturday, he had shown good climbing legs, finishing fourth on stage 14 behind Pogacar, Del Toro and Paul Seixas.
Fractured collarbone
After the stage concluded with Remco Evenepoel winning in front of Pogacar and Del Toro, Vingegaard's team announced that he had suffered a fractured collarbone from the fall.
In a social media post, they said: "Following a crash in Stage 15 of the Tour de France, Jonas sustained a fractured collarbone and multiple abrasions.
"Due to the severity of the collarbone fracture, surgical intervention has been recommended and will be performed in the coming days."
It was the first time that Vingegaard has left the Tour early, having never finished lower than second place at the race.