The outbreak has prompted restrictions on the movement of the big birds and their products in the Western Cape, the provincial ministry of agriculture said in a statement on Tuesday.
Tests samples from an ostrich farm near Oudtshoorn, found the presence of the H7N1 virus, the ministry said.
Another strain, H7N9, has killed eight people in eastern China since it was confirmed in humans for the first time last month.
Marna Sinclair, a state vet, said there had been previous incidents of H7N1 viruses in the region, but that none were found to be related to the current Chinese strain and no people have fallen ill.
"There is no real concern. We doubt it is a related virus but are conducting tests to make sure," she said.
Two years ago, 10 000 ostriches were culled after an outbreak of another, less virulent form of bird flu halted ostrich-meat exports to the European Union.