The variant discovered in southern African states has been identified in a person who returned from Malawi, the health ministry said.
Israel has identified a case of a Covid-19 variant with a large number of mutations first detected in South Africa.
"The variant discovered in southern African states has been identified in Israel," the health ministry said on Friday, adding it was recorded "in a person who returned from Malawi".
Two more suspected cases were detected in "people returning from abroad", it said, adding that they had been placed in quarantine.
The three people were all vaccinated, the health ministry said, without specifying the number of doses or the type of vaccine.
Scientists in South Africa said on Thursday that they had detected the new B.1.1.529 strain with at least 10 mutations, compared with two for Delta or three for Beta.
The variant was of "serious concern" and had been blamed for a surge in infection numbers, the authorities in South Africa said.
It had also been detected in Botswana and Hong Kong among travellers from South Africa, they said.
Israel was one of the first countries to launch vaccines against the coronavirus last year, thanks to a deal with Pfizer that gave it access to millions of doses in exchange for data on the vaccine's efficacy.
Its initial vaccine rollout of the Pfizer-BioNTech jab was among the world's fastest, and more than 5.7 million of the country's nine million people are now fully vaccinated.