South Africa’s Health Ministry says the decision is based on a trial that found the vaccine offers limited protection for the more contagious variant circulating in the country.
South Africa has suspended the start of its AstraZeneca inoculation programme over concerns the shot does not work on a new variant.
The country's health ministry will meet with WHO experts on Monday to discuss the vaccine which is already facing questions about its efficacy for over-65s.
A trial showed the vaccine provides only "minimal" protection against mild to moderate Covid-19 caused by the variant first detected in South Africa, a setback to the global fight against the pandemic as many poorer nations are relying on the logistical advantages offered by the AstraZeneca shot.
Africa's hardest-hit nation was due to start its campaign in the coming days with a million AstraZeneca doses but the government decided to hold off in light of the results from the trial conducted by the University of Witwatersrand in Johannesburg.
"It's a temporary issue that we have to hold on AstraZeneca until we figure out these issues," Health Minister Zweli Mkhize told reporters on Sunday.
The 1.5 million AstraZeneca vaccines obtained by South Africa, which will expire in April, will be kept until scientists give clear indications on their use, he added.
AstraZeneca, which developed the shot with the University of Oxford, told AFP: "We do believe our vaccine will still protect against severe disease."
A company spokesperson said researchers were already working to update the vaccine to deal with the South African variant, which has been spreading rapidly around the world.
A World Health Organization panel is also meeting on Monday in Geneva to examine the shot, which is a major component of the initial Covax global vaccine rollout that covers some 145 countries, mostly lower- and lower-middle income economies.
Out of the initial 337.2 million Covax doses, 240 million are AstraZeneca shots, which do not require the supercold storage needed for the Pfizer and Moderna vaccines.
There were already concerns about the efficacy of the AstraZeneca shot among over-65s, with a number of European nations not authorising it yet for that demographic.
'Effective in primary objective'
Australia moved to reassure its citizens over the efficacy of AstraZeneca's Covid-19 vaccine after South Africa suspended use of the shot.
Australia's Minister for Health, Greg Hunt, said the vaccine is effective in its primary objective.
"There is currently no evidence to indicate a reduction in the effectiveness of either the AstraZeneca or Pfizer vaccines in preventing severe disease and death. That is the fundamental task, to protect the health," Hunt told reporters in Canberra.
Australia is expected approve the use of the AstraZeneca vaccine within days. Last month, it approved the use of the Pfizer-BioNTech Covid-19 vaccine, although it has secured enough doses for less than half of its population and orders remain delayed.
Australia is expected to begin using the Pfizer vaccine later this month though Canberra's hopes for a complete inoculation programme rests with the AstraZeneca vaccine.
The country has ordered 53 million doses of the AstraZeneca vaccine, the vast majority of which will be manufactured locally by CSL Ltd.