Currently South African citizens can only apply for a visa to Australia via their local Australian embassy.
The Australian ETA (Online visa) is not yet available, see below for Australian Embassies in South Africa.
Australian High Commission, Pretoria
292 Orient Street
Telephone: 27 12 423 6000
Australian Trade Commission, Johannesburg
Corner of Maud & 5th Street
Telephone: 27 11 911 4500