The 53-year-old man, who died Tuesday in Rio de Janeiro, had an operation in mid-October at a Johannesburg hospital which treated several cases of a new arenavirus strain which killed four people.
But South Africa's National Institute for Communicable Diseases, which is working with their Brazilian counterparts, said it was unlikely that he had been infected with the same virus.
"He did not have contact with any of the patients who had the arenavirus infection," said Lucille Blumberg, the institute's deputy director.
"The time from any possible exposure to the virus to the development of symptoms ... would be less than 21 days, and the time from his admission there to development of his current illness is in excess of this period."
Tests for the arenavirus conducted at the US Centres for Disease Control and Prevention in Alanta would "definitely exclude the diagnosis," Blumberg said.
Rio de Janeiro's state health ministry said the man, whose name was not released, died Tuesday after falling ill on November 25, two days after arriving in Brazil to attend conferences.
He was taken to hospital with fever, vomiting, blood in his urine and rashes.
Doctors suspected he had contracted an arenavirus, a highly contagious group of viruses that includes Lassa fever, an infection endemic to west Africa that typically spreads to humans from proximity to rodents or from infected people's secretions.
"While the cause of his illness is not at this stage known, investigations are ongoing to define a case," Blumberg said.
The recent arenavirus scare in South Africa was first identified in a woman airlifted from Zambia, and also killed a member of the medical staff who accompanied her, a nurse and a hospital cleaner.