The first ODI will now be played on December 6 in Paarl, followed by games on the 7th and 9th.
The first one-dayer was called off just an hour before the toss with the news of a positive case within the home team camp after mandatory testing procedure in the hotel premises.
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The England team then raised concerns over the bio-security arrangements for their tour while the South Africans launched an investigation on how one of their own caught the dangerous virus.
"The entire Proteas team has returned negative results from the COVID-19 tests that were conducted yesterday evening in Cape Town ahead of the three-match One-Day International (ODI) series," Cricket South Africa (CSA) said in a statement.
This was the third instance of an unnamed player of South Africa testing positive before or during England's tour, which is providing a much-needed financial balm to the struggling CSA.
Proteas team doctor Shuaib Manjra admitted they don't yet have any explanation as to how a member of the Proteas camp contracted COVID-19 while staying in a hotel shared by both the sides.
"We have spoken to the player, looked at security cameras and other information, and we have not been able to date to identify where that source was. But clearly, it is cause for concern," he said in response to rumour that a player had left the hotel without clearance.
"I can categorically state that no player is able to leave the hotel environment. The security will not allow the player to leave, unless he is doing so in an assigned, official vehicle," added Dr Majra.
The second and third ODIs will be played in Cape Town on Monday (December 7) and Wednesday (December 9), respectively.
(Inputs from Reuters)