The two men, who have not yet been identified, had taken off from Dortmund in Germany yesterday, according to the Chambery prosecutor who is investigating the cause of the accident in the Savoie region of eastern France.
The two-seater tourist plane was heading to the French city of Albertville and a search began yesterday evening when it failed to land as scheduled.
The wreckage was spotted on Mount Trelod in the Bauges mountains with an altitude of around 2,200 metres.
Rescuers on the ground brought down the bodies of the two victims on Saturday.
An autopsy will be carried out Monday to determine if either of the pilots had fallen ill.