It was not immediately clear how many of the infections were caused by Omicron, given only a fraction of samples are sequenced, but experts believe it is driving South Africa's fourth wave of infections.
The statistics from the National Institute for Communicable Diseases (NICD) brought the confirmed number of cases in the country to 3.071 million, with more than 90,000 COVID-linked deaths since the pandemic started.
Early evidence suggests Omicron is more transmissible than any previous variant, but that symptoms may be less severe, with lower levels of hospitalisation, especially in vaccinated patients.
But the economic fallout for South Africa - which has been hit by international travel bans since its scientists correctly identified the variant late last month - has been devastating.
President Cyril Ramaphosa was due to meet with senior officials in charge of the COVID-19 response this week, and will decide on whether to tighten low-level lockdown restrictions. That seems unlikely, as hospital capacity is far from being overwhelmed, as it was in previous waves.
South African health regulator SAHPRA on Wednesday approved a third or booster shot of Pfizer's COVID-19 vaccine for adults and children over the age of 12 years.