The baby was born preterm with lung difficulties and had to put on a ventilator, according to a statement from the health ministry.
The baby is among the 27 coronavirus deaths announced Wednesday, bringing the total number to 339, according to the ministry.
With more than 18,000 cases, South Africa has the highest number of coronavirus patients on the continent.
Health minister Zweli Mkhize said he was devastated by the death of a health worker in the Western Cape province — the virus epicenter in South Africa — and paid tribute to professionals on the frontline of the country’s response to the outbreak.
The country imposed strict restrictions, including a five-week lockdown which ended April 30, to combat the spread of the disease.
As the country began easing restrictions in May, South Africa’s President Cyril Ramaphosa said the nation has adopted a five-level alert system to respond to the pandemic that will allow certain sectors of the economy to resume phased operations.
The government plans to reopen schools on June 1 and says the education department will roll out guidelines for the resumption.