But the British company said early data from the study, due to be published on Monday, has shown the jab can protect against severe disease caused by the mutation.
The study, first reported by the Financial Times, into the E484K mutation involved some 2,000 people, most of whom were young and healthy.
"We do believe our vaccine could protect against severe disease, as neutralising antibody activity is equivalent to that of other Covid-19 vaccines that have demonstrated activity against more severe disease, particularly when the dosing interval is optimised to eight to 12 weeks," a spokesman reportedly said.
It comes after research released on Friday indicated that the Oxford/AstraZeneca jab is effective at fighting the new UK coronavirus variant.
Andrew Pollard, professor of paediatric infection and immunity, and chief investigator on the Oxford vaccine trial, said: "Data from our trials of the ChAdOx1 vaccine in the United Kingdom indicate that the vaccine not only protects against the original pandemic virus, but also protects against the novel variant, B117, which caused the surge in disease from the end of 2020 across the UK."
Professor Robin Shattock, who is leading Covid-19 vaccine research at Imperial College London, urged caution about the findings.
He told BBC Breakfast: "It's a very small study with just over 2,000 people and it's not published so we can only judge it from the press release and press coverage. But it is concerning to some extent that we're seeing that it's not effective against mild or moderate disease."
Prof Shattock said the study participants had a mean age of around 31 and it is not yet clear how many had two doses, and at what intervals.
He continued: "Oxford, as well as other groups, are already working on vaccines against these variants... we will need to keep updating the vaccines to keep ahead of the virus."
Professor Anthony Harnden, deputy chair of the Joint Committee on Vaccination and Immunisation, said: "Evidence suggests the Oxford/AZ vaccine protects against disease caused by the predominant Covid variants circulating in the UK.
"It remains highly likely that the vaccine will also protect against severe disease caused by the South African variant."
Also on Friday, public health officials said the outcomes of targeted tests to track the South African variant in England could take up to two weeks.
Door-to-door testing as part of urgent efforts to swab 80,000 people came after 11 cases of the variant were identified in the previous few days in people who had no links to travel - suggesting it may be spreading in communities.