As per a CSA release, the decision was taken jointly by the two boards to ensure the mental and physical health and welfare of players from both teams.
The players and management are now self-isolating in their rooms until further advice from the medical teams, the ECB said.
England had white-washed South Africa in the shortest format after registering a thumping nine-wicket win in the third T20I.
The player, who was not named, is the third South African player to test positive during the England tour, which began in mid-November.
Along with du Plessis, Kagiso Rabada, Pite van Biljon, Bjorn Fortuin and Reeza Hendricks have also been released from the squad.
South Africa pacer Kagiso Rabada has been ruled out of the upcoming three-match ODI series against England due to an injury.
The England squad has arrived in South Africa to begin their preparations and will play a Tour match on Saturday.
On Thursday, the CSA's Members' Council decided not to appoint the interim board citing an inability to work with them.
England were cruising to victory at 232 for four after leg-spinner Adil Rashid and his fellow slow bowlers restricted South Africa to 256 for seven after they were sent in to bat. But...
The veteran seamer is making a comeback to the international cricket after nearly a year as he was recovering from a recurring shoulder injury.
Now retired South Africa great Kallis was an outstanding all-rounder, scoring 45 Test hundreds and averaging more than 55.
Faf du Plessis said the tourists were determined to avoid a repeat of the silly mistakes that had cost them dear at Headingley.