It is the second time the Springboks have been forced to take preventative measures ahead of their upcoming series with the British and Irish Lions.
Vincent Koch, Herschel Jantjies and Sbu Nkosi tested positive for COVID-19 on 28 June, though the world champion resumed training and its first warm-up match – a 40-9 victory over Georgia – went ahead as planned last Friday.
However, this Friday's game against the same opponents is now in jeopardy following another positive case, which also raises further questions about the three-match Test series with the Lions.
A statement from SA Rugby on Monday read: "Springbok training has been suspended for Monday following a positive test for COVID-19 in the squad.
"The players have been placed in preventative isolation prior to further PCR testing and a review of the testing data by the Medical Advisory Group (MAG).
"Lood de Jager returned a positive outcome in scheduled testing and, because of his close contact with a number of squad members, the entire group has gone into isolation.
"An update will be issued following the review by the MAG and the further testing."
South Africa's victory over Georgia was their first match since winning the World Cup in November 2019.
Its first Test with the Lions is due to take place on July 24 in Cape Town, before moving to Johannesburg for the second and third matches.