Jo van Niekerk, a 29-year-old zoology student, was arrested in November after the animals were found in his baggage and clothing at the airport.
Van Niekerk's lawyer says he will appeal Tuesday's ruling, though acknowledges the verdict could have been worse.
Police officials say a separate arrest warrant has been issued for an alleged accomplice who they say is on the run.
Madagascar, an island in the Indian Ocean off the southeastern coast of Africa, is home to a number of animals found nowhere else in the world.
