Flight arrivals will be banned from the key tourist destination between 12 noon on Friday and 4am on Sunday while quarantine hotel accommodation is prepared.
The health secretary, Sajid Javid, said: “As part of our close surveillance of variants across the world, we have become aware of the spread of a new potentially concerning variant.
“We are taking precautionary action to protect public health and the progress of our vaccine rollout at a critical moment as we enter winter, and we are monitoring the situation closely.”
The UK Health Security Agency (UKHSA) has designated it a “variant under investigation”. The chief executive, Dr Jenny Harries, said: “This is the most significant variant we have encountered to date and urgent research is underway to learn more about its transmissibility, severity and vaccine-susceptibility.”
Two British Airways overnight flights from London Heathrow, BA43 to Cape Town and BA55 to Johannesburg, took off shortly before the announcement was made.
Passengers booked to return to the UK while South Africa is on the red list will learn on arrival that they face hotel quarantine when they return at a cost of over £2,000.
A spokesperson for British Airways said: “Following the latest announcement from the health secretary we’re working through plans for our customers and colleagues currently in South Africa and those due to travel from the UK in the coming days.
“We’ll be contacting affected customers with information about their flight.”
Virgin Atlantic’s departure from Heathrow to Johannesburg departed an hour late, at 11.30pm on Thursday. It appears passengers were informed about the requirement for hotel quarantine on their return, and given the option to offload rather than face hotel quarantine on their return the UK.
Namibia, Lesotho, Botswana, Eswatini and Zimbabwe will also be added to the red list. None has direct links with the UK.
UK scientists sounded the alarm on Thursday night over the B.1.1.529 variant, which has the potential to evade immunity built up by vaccination or prior infection.
While no cases have been found in Britain, officials raised concern over a rapid rise in cases in South Africa.
One senior UKHSA expert said: “This is the worst variant we have seen so far.”
Only 59 confirmed cases have been identified in South Africa, Hong Kong and Botswana.
The variant has over 30 mutations – around twice as many as the Delta variant – which could potentially make it more transmissible and evade the protection given by prior infection or vaccination.
The UK government announcement has been met with despair by the travel industry, as it mirrors the ban imposed on South African flights almost a year ago because of fears of what became known as the Beta variant.
Julia Lo Bue-Said, chief executive of the Advantage Travel Partnership, said: “We all accept the government must make decisions in the interest of public health.
“However, some 20 months into the crisis, and six weeks after taking South Africa and its neighbours off the red list, it just feels like deja vu.
“The communication process is a shambles – relying on a tweet from the health secretary is no way to update the public.”
Paul Charles, chief executive of the travel consultancy, the PC Agency, said: “Yet again the government is falling back on widespread country measures rather than assessing individual risk.
“There is currently no evidence that fully-jabbed citizens are at risk from this apparent new variant. So it seems a strange backward step to take.”
South Africa was effectively off-limits to British travellers for almost a year. It was taken off the red list last month.