Froome's Twitter account later confirmed he was undergoing surgery to fix "multiple fractures".
Tour de France director Christian Prudhomme was swift to wish Froome a speedy recovery.
Britain's four-times victor of the Yellow Jersey was airlifted to hospital with multiple injuries - including a broken leg, broken elbow and fractured ribs - after a crash that shook cycling.
But all indications were that Froome had done enough to be Ineos' unofficial leader at the Tour, ahead of both Thomas and Bernal, as he aimed for an historic fifth title. The Tour de France won't be the same without him. He was treated quickly by race paramedics who happened to be nearby in Roanne, a town in central France, and was airlifted to St Étienne University Hospital for further treatment.
Froome's injuries, which will nearly certainly rule him out of the world championships in Yorkshire in September, stunned Tour de France organisers.