It is the first case in southern Africa, and the latest confirmed case in sub-Saharan Africa after Nigeria and Senegal.
The case was detected in the country's eastern Kwa-Zulu Natal province.
The patient and his wife were part of a group of 10 people who arrived back in South Africa from Italy on March 1.
South Africa on Thursday confirmed its first case of the novel coronavirus, a 38-year-old male who travelled to Italy, health ministry announced.
It is the first case in southern Africa, and the latest confirmed case in sub-Saharan Africa after Nigeria and Senegal. "This morning,... the National Institute for Communicable Diseases confirmed that a suspected case of COVID-19 has tested positive," Health Minister Zweli Mkhize said in a statement.
The case was detected in the country's eastern Kwa-Zulu Natal province.
The patient and his wife were part of a group of 10 people who arrived back in South Africa from Italy on March 1.
Two days later, on March 3, he consulted a private general practitioner with a fever, headache, sore throat and a cough.
Italy has emerged as the European hotspot for the deadly virus with the national death toll at 107, the deadliest outbreak outside China.
More than 90,000 people have been infected and over 3,000 killed worldwide since the virus first emerged in China in December.
South Africa is preparing to repatriate 184 of its citizens—comprising students, teachers and other professionals working in China's Wuhan, the epicentre of the epidemic.
The government's information department also announced that two South Africans working on the cruise ship Diamond Princess who had initially tested positive for the virus, "have now tested negative and will shortly be making their way home".