The South African Health Products Regulatory Authority (Sahpra) said it made the decision after the US Food and Drug Administration (FDA) raised concerns over manufacturing practices at the Baltimore plant.
"Sahpra reviewed the data provided by the FDA and has made a decision not to release vaccine produced using the drug substance batches that were not suitable,” Sahpra said in a statement.
The findings by the FDA would impact two million vaccines that are awaiting release at Aspen Pharmacare's Gqeberha manufacturing site, acting health minister Mmamoloko Kubayi-Ngubane said on national broadcaster, SABC.
Kubayi-Ngubane said the government was in talks with J&J over replacing the affected vaccines.
Fears of a third Covid-19 wave are mounting in the country, which has recorded the highest number of infections and deaths on the continent, with daily infections rising to over 9,000 per day.
South Africa launched phase two of its vaccine rollout in May, aiming to inoculate fiv- million people aged over 60 by the end of June.
Local heath regulators said 300,000 doses of the J&J vaccine have been cleared by the FDA and will be shipped to South Africa.
Manufacturing at the Baltimore plant was halted in April after it was discovered that ingredients from AstraZeneca's Covid-19 vaccine, produced at the plant at the time, had contaminated a batch of J&J's vaccine.
A further inspection by the FDA also turned up a long list of sanitary problems and bad manufacturing practices at the Emergent plant.
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