It had a large number of mutations, and early evidence suggested an increased reinfection risk, the WHO said.
It was first reported to the WHO from South Africa on 24 November, and has also been identified in Botswana, Belgium, Hong Kong and Israel.
A number of countries around the world have now decided to ban or restrict travel to and from southern Africa.
Travellers from South Africa, Namibia, Zimbabwe, Botswana, Lesotho and Eswatini will not be able to enter the UK unless they are UK or Irish nationals, or UK residents.
US officials said flights from South Africa, Botswana, Zimbabwe, Namibia, Lesotho, Eswatini, Mozambique and Malawi would be blocked, mirroring earlier moves taken by the EU. It will come into effect on Monday.
On Friday, the WHO said the number of cases of this variant, initially named B.1.1.529, appeared to be increasing in almost all of South Africa's provinces.
"This variant has a large number of mutations, some of which are concerning," the UN public health body said in a statement.
It said "the first known confirmed B.1.1.529 infection was from a specimen collected on 9 November".
The WHO said it would take a few weeks to understand the impact of the new variant, as scientists worked to determine how transmissible it was.
More about: WHO coronavirus
