Veterinarians from the provincial department of agriculture detected Highly Pathogenic Avian Influenza (HPAI) during routine testing.
Winde says the tests for the highly contagious strain at the Southern Cape farms came back positive.
"Both farms were placed under quarantine immediately".
An announcement of the outbreak by South Africa in June prompted some neighboring countries to temporarily suspend imports of poultry from the country.
At this stage, it appears that the incidence has been confined to the two properties.
It is suspected that wild birds are the source of the infection. Current practice in most regions of the world requires the culling of infected birds. The outbreaks involved seven commercial chicken farms, two groups of backyard chickens, three sets of wild birds and one group of domestic geese.
The department says ostrich and chicken meat is safe for human consumption.
"The department has received requests to vaccinate and these requests are under consideration. At the moment‚ vaccination against highly pathogenic avian Influenza is prohibited for the long term benefit of the poultry industry at large‚" said Molapo.
Poultry vaccines can prevent healthy chickens from contracting deadly strains of bird flu.
"Quarantine has been instituted and the application of disease control measures have commenced", the Department of Agriculture, Forestry and Fisheries said in a statement. The continued cooperation of the public and the poultry industry, in the timeous reporting of sick and dying birds to Government Veterinary Services, is vital for the speedy response and the necessary investigations in order to effectively manage the disease threat.