“As it stands as a country we now meet that criteria,” said Zweli Mkhize in a statement as the country registered nearly 7,000 new cases in the last 24-hour cycle.
The country now counts 828,598 infections after 6,709 new cases were detected between Tuesday and Wednesday.
South Africa had reined in its first wave which occurred in July at an average of 12,000 cases detected daily.
Numbers then gradually came down, at a point dropping below 1,000 in September.
The minister said the number of new infections detected in parts of the country suggest that “we should expect faster rising numbers with a higher peak than in the first wave”.
Most of the cases have been detected in the southern parts of the country, including Cape Town.
Mkhize said the new cases recorded over the last two days have mostly been found in the 15-19 year age group.
The infections are believed to have been fuelled by recent “super spreader” year-end parties where young people drank alcohol and failed to wear masks or keep social distancing.
President Cyril Ramaphosa has warned that the second wave of coronavirus infections would “choke” economic recovery.
The country accounts for more than a third of the cases reported across the African continent.