Nearly 50 tests were conducted before players and support staff entered their bio-secure base in Cape Town for the series featuring three Twenty20 Internationals followed by an equal number of one-dayers.
"One player has returned a positive test result and two players were considered close contacts based on the risk assessment undertaken by the medical team," Cricket South Africa (CSA) said in a statement on Wednesday.
"All three players have been placed in immediate isolation in Cape Town as part of the COVID-19 protocols. While all players are asymptomatic, CSA's medical team will monitor them to ensure their health and well-being."
The three were not identified.
South Africa have not named any replacement but two new players will join the group for the inter-squad practice matches on Saturday.
The series, which will be played behind closed doors, gets underway with the first Twenty20 match in Cape Town on Nov. 27. (Reporting by Amlan Chakraborty in New Delhi Editing by Robert Birsel)