Players Thabiso Monyane and Kamohelo Mahlatsi and video analyst Mario Masha are now in the Tokyo 2020 isolation facility, a Team South Africa statement said on Sunday.
A fourth member of the country's Olympic delegation, rugby coach Neil Powell, also tested positive while at a training camp in the city of Kagashimo in southern Japan and is in isolation there.
The statement further shows that Monyane and Mahlatsi are the first athletes to test positive while staying at the Olympic Village, which has been set up as a bubble in hopes of preventing the spread of disease among the 11 000 people travelling from around the world to compete in the games.
According to South African officials, the positive results came up in daily testing, and the men had previously tested negative on their daily tests, as well as when they left South Africa.
“The timing of the positive results suggests that the PCR test in these individuals was done during the incubation period of the infection, which is how they could be negative in South Africa and then positive in Japan,” Team SA chief medical officer, Dr Phatho Zondi said in the statement.
All other members of the SA team have continued to test negative.