"We can confirm that this diplomat has been expelled. He left the country on the 11th of December," Nelson Kgwete told AFP.
Kgwete said the diplomat was arrested in neighbouring Mozambique in May on charges related to rhino horn smuggling.
At the time of arrest, he was driving a vehicle with a South African diplomatic registration.
South Africa's News24 said the diplomat was arrested after 4.5 kilogrammes of rhino horn and USD 99,300 in cash were found in his car. The news website added that Mozambican police released the man on USD 30,000 bail.