The country’s health ministry said the infected person was identified as a traveller who had returned from Malawi.
Two further suspected cases have been placed in isolation, the ministry said in a statement on Thursday. All three travellers were vaccinated but their exact vaccination status is unclear.
The new B.1.1.529 variant, first detected in Botswana, has sparked alarm among scientists due to its high number of mutations. Senior scientists have said it is the worst strain they have seen so far during the pandemic.
Late on Thursday, the government declared South Africa and six other African nations to be "red countries" from which foreign nationals are barred from entering Israel. The UK Government introduced similar restrictions.
Israelis returning from those countries must spend between 7-14 days in a quarantine hotel after arrival.
South Africa has confirmed around 100 infections as B.1.1.529, but the variant has also been found in Botswana and Hong Kong, with the Hong Kong case a traveller from South Africa.
It comes just two months after a fourth wave of cases in Israel driven by the Delta variant began to subside.
Despite a fast start to their vaccination programme last year, around 64 per cent of the country is fully jabbed – well below the UK and many other EU countries.
However, the country’s decision to rollout its booster campaign earlier than other countries has proved successful. Nearly half the population has received a third vaccine dose, which has kept hospitalisations at a manageable level.
The variant has 30 mutations and a spike protein that is dramatically different to the one in the original coronavirus that Covid vaccines are based on, the UK Health Security Agency (UKHSA) said.
The chief medical adviser of the UKHSA Dr Susan Hopkins warned that the mutations of the variant were “highly complex” and “challenging”.
“We don’t know how they are going to interact in common,” she added.
European Commission President Ursula von der Leyen said the EU would propose a strict ban on travel from the affected region in southern Africa. Germany, Italy and the Netherlands have already announced travel restrictions.
However, one epidemiologist said it may be too late to tighten travel curbs.
"I think we have to recognise that most likely this virus is already in other places. And so if we shut the door now, it’s going to be probably too late," said Ben Cowling of the University of Hong Kong.