The Frenchman, 33, fell heavily around 100km from the finish in an incident that also ended Andy Schleck's race.
Voeckler was immediately taken to hospital and is expected to be out for at least a fortnight, depending on how serious the fracture proves to be.
Reports that he had also suffered a broken leg were denied by his team.
Schleck was not thought to have been seriously injured.
Katusha Joaquim Rodriguez also tumbled during the race but he only suffered a thigh injury.