Officials have emphasized that no humans have been affected.
The Agriculture Department says that exports of processed poultry products, live chickens and fresh produce will continue, depending on the requirements of importing countries.
Last week, South Africa reported an outbreak of a highly pathogenic H5N8 bird flu at a farm in the Free State province, an agricultural industry body group, AgriSA, said.
Earlier this month, all trade was suspended in birds and chicken products from neighbouring Zimbabwe after it reported an outbreak of H5N8 at a commercial poultry farm.
