The court in Jodhpur also fined him 10,000 rupees ($154; £109) for the crime. He has since been taken to jail.
Khan killed the two blackbucks, a protected species, in the western state of Rajasthan while shooting a film.
Four other actors who starred with him in the movie and were also charged with the offence have been acquitted.
Khan, 52, can appeal against the verdict in a higher court.
Correspondents say he will have to spend at least a few days in prison.