"The condition of the patient is stable and the results of the Ebola virus disease are negative," spokesman Joe Maila said in a statement.
"We have also conducted the tests for malaria and the results are also negative."
Further tests were being carried out to check for other infections. The 37-year-old man, who worked as a health and safety officer in a mining operation in Liberia, was admitted to hospital on Sunday. He returned to South Africa on August 6.
The man had no contact with any patients in Liberia. He was fine on arrival in the country, but on August 16 he became feverish and went to his doctor.
He went home and was monitored, but when his temperature increased he was taken to hospital for further assessment.
"As a precautionary measure, given his history of working in Liberia, the protocol developed for haemorrhagic fevers needed to be followed," Maila said on Sunday.
On August 14, Health Minister Aaron Motsoaledi said there were no known Ebola cases in South Africa.
A pregnant Guinea woman, suspected to have been infected with the virus, had tested negative for Ebola. She was admitted to Rahima Moosa Mother and Child Hospital because of a severe fever during labour.
Maila on Monday said a team from the National Institute for Communicable Diseases had been dispatched to Sierra Leone with the necessary equipment to assist in containing Ebola in that region.