At 1534 GMT, the rand traded at 15.8000 against the dollar, 1.56% firmer than its previous close of 16.0500.
Data from South Africa's National Institute for Communicable Diseases showed on Wednesday that 74% of all the virus genomes it had sequenced last month had been of the new variant, as new cases doubled from Tuesday.
The data also showed that the Omicron variant appeared able to get around some immunity but vaccines should still offer protection against severe disease.
On Thursday a scientist studying the outbreak of the new strain said symptoms for reinfected patients and those infected after vaccination appear to be mild.
"If evidence grows that the current vaccines will also work against the latest variant ... the general risk-off bias is likely to be short-lived," analysts at Oxford Economics Africa said in a note.
The strain has been found in places as widespread as Australia, Britain, Canada and Japan, even as those countries rapidly tighten their borders.
Stocks however, took a breather, reversing gains from previous sessions as some uncertainty over Omicron lingered and as South Africa saw an increase in COVID-19 reinfections due to the new variant.
The Johannesburg All-Share index closed 0.25% weaker, while the Top-40 index dropped 0.36%.
Leading the decliners were gold stocks, tracking weaker bullion prices. Gold struck a one-month low on Thursday as U.S. Federal Reserve Chairman Jerome Powell's comments on the need to tame inflation bolstered bets for faster monetary policy tightening and offset Omicron-driven safe-haven inflows into bullion. [GOL/]
The mining index fell 1.72%, led by AngloGold Ashanti, which was down 5.33%.
(Reporting by Olivia Kumwenda-Mtambo and Nqobile Dludla ; Editing by Subhranshu Sahu and Mark Porter)