"The first people who will qualify for the booster dose in South Africa will be people over the age of 60 years," Dr Nicolas Crisp, director general at the health ministry, told a weekly news conference.
Experts are working to determine whether current Covid vaccines will work against the new highly-mutated variant, which was discovered by South African scientists last month.
The daily number of new Covid infections surged to a high of 22,391 on Thursday, when nearly 30 percent of tests were positive.
The highest daily tally so far was in early July, when the country hit more 26,000 new infections.
Health practitioners last month had already started being offered Johnson & Johnson shots as boosters.
South Africa is the worst-hit country in the continent for coronavirus, recording a cumulative 3.09 million cases, of which over 90,000 have been fatal.
A small study this week by the country's African Health Research Institute, not yet peer reviewed, suggested that Omicron may be able to evade some of the antibody immunity from the Pfizer-BioNTech vaccine.
But, its authors said, there was no reason to believe that vaccination would not protect against severe disease caused by the variant.
Slightly more than a quarter of South Africa's population is fully vaccinated, with the figure among adults being 43 percent.
Omicron accounts for around 70 percent of new infections being detected in South Africa, Health Minister Joe Phaahla has said.
However, hospitalised patients are so far showing mild symptoms, he said.
For an optimal experience, please
