Health Minister Zweli Mkhize said 844 more people have died from Covid-19 by Wednesday.
"Today we have reached a grim milestone as we breach the 20 000 mark for new cases identified in 24 hours," Mkhize said in an uncharacteristically late update on the situation.
He said 21 832 new cases were also identified.
This brings the total number of cases in South Africa to 1 149 591.
The total recorded death toll is 31 368.
Of the 844 people who died, 452 were in the Eastern Cape, 12 in the Free State, 96 in Gauteng, 65 in KwaZulu-Natal, 11 in Limpopo, eight in Mpumalanga, 46 in North West, five in the Northern Cape and 149 in the Western Cape.
Mkhize said the 452 deaths reported in the Eastern Cape were due to data reconciliation between May and November 2020. He said it included analysis of community cases in which post-mortem swabs were taken for testing and analysis of clinical records where the diagnosis was unconfirmed at the time of death.
He said the health department is engaging the province to investigate the details of the reporting backlog.
Recoveries are at 929 239 and the recovery rate is 80.8%.