Prime Minister Naftali Bennett said in a statement that the ban, pending government approval, would last 14 days. Officials hope that within that period there will be more information on how effective COVID-19 vaccines are against Omicron, which was first detected in South Africa and has been dubbed a "variant of concern" by the World Health Organization.
"Our working hypotheses are that the variant is already in nearly every country," Interior Minister Ayelet Shaked told N12's Meet the Press, "and that the vaccine is effective, although we don't yet know to what degree."
Israelis entering the country, including those who are vaccinated, will be required to quarantine, Mr Bennett said. The ban will come into effect at midnight on Sunday. A travel ban on foreigners coming from most African states was imposed on Friday.
Omicron testing underway after passengers with COVID-19 arrive in Sydney from Africa
The Shin Bet counter-terrorism agency's phone-tracking technology will be used to locate carriers of the new variant in order to curb its transmission to others, Mr Bennett said.
Used on and off since March 2020, the surveillance technology matched virus carriers' locations against other mobile phones nearby to determine with whom they had come into contact. Israel's Supreme Court this year limited the scope of its use after civil rights groups mounted challenges over privacy concerns.
Israel has so far confirmed one case of Omicron.
The highly infectious variant, which has also been detected in Belgium, Botswana, Hong Kong, Italy, Germany and Britain, has sparked global concern and a wave of travel curbs, although epidemiologists say such restrictions may be too late to stop Omicron from circulating globally.
Dutch authorities have quarantined 61 passengers from South Africa who tested positive for COVID-19.
South Africa complained it was being "punished" with air travel bans for having first detected the strain, which the World Health Organization (WHO) has termed a "variant of concern".
A series of countries across the world began restricting travel from the region, to try to head off any threat to global efforts against the pandemic.
Scientists are racing to determine the threat posed by the heavily mutated strain, particularly whether it can evade existing vaccines. It has already proved to be more transmissible than the dominant Delta variant.
Travellers thronged Johannesburg international airport, desperate to squeeze onto the last flights to countries that had imposed sudden travel bans. Many had cut short holidays, rushing back from South African safaris and vineyards.
"It's ridiculous, we will always be having new variants," British tourist David Good told AFP, passport in hand. "South Africa found it, but it's probably all over the world already."
The virus has already slipped through the net, with cases discovered in Europe, Hong Kong and Israel as well as in southern Africa.
Britain on Saturday announced tougher entry rules for all arriving passengers and the return of a masks mandate, after confirming its first two cases of the new Omicron strain of COVID-19.
Prime Minister Boris Johnson said face masks would again be required in shops and on public transport.
Germany confirmed its first two cases of the Omicron variant in travellers who arrived at Munich airport from South Africa.
Italy announced its first case of the new Covid strain in a traveller from Mozambique.
And Dutch officials said the new Omicron variant was "probably" among 61 passengers who had arrived on two flights from South Africa a day before and who tested positive for COVID-19.
The two KLM flights, which took off before the Dutch announced their ban on travellers from the region, were being kept quarantined in a hotel.
The US was warning against travel to eight southern African countries over Omicron concerns after the White House announced new restrictions in response to the new COVID-19 variant.
Already on Friday Belgium announced its first case in an unvaccinated person returning from abroad.
The Czech Republic was carrying out further tests on a woman who had travelled from Namibia and was suspected to have the new variant, prime minister Andrej Babis said.
The WHO said it could take several weeks to understand the variant, which was initially known as B.1.1.529, It cautioned against travel curbs while scientific evidence remains scant.
WHO says variant is of 'concern', names it 'Omicron'
South Africa called the travel curbs "draconian" and on Saturday said the flight bans were akin to punishing South Africa for its advanced genomic sequencing and the ability to detect new variants quicker.
"Excellent science should be applauded and not punished," the foreign ministry said in a statement.
The main countries targeted by the shutdown include South Africa, Botswana, Eswatini (Swaziland), Lesotho, Namibia, Zambia, Mozambique, Malawi and Zimbabwe.
US President Joe Biden meanwhile said richer countries should donate more COVID-19 vaccines and give up intellectual property protections to manufacture more doses worldwide.
"The news about this new variant should make clearer than ever why this pandemic will not end until we have global vaccinations," he said.
The WHO used the news to push vaccine equity, saying more COVID-19 transmission created more opportunity for new variants to emerge.
With memories still fresh of the way global air travel helped the spread of COVID after it first emerged in the Chinese city of Wuhan in late 2019, countries clamped down swiftly.
Australia and Belgium became the latest to act, banning all flights from nine southern African countries.
South Korea and Thailand restricted flights from eight countries, as did the United States, Brazil, Canada and Saudi Arabia.
EU officials agreed in an emergency meeting to urge all 27 nations in the bloc to restrict travel from southern Africa. Many members had already done so.
The World Trade Organization called off a ministerial conference, its biggest gathering in four years, at the last minute Friday due to the new variant.
Vaccine manufacturers have held out hope that they can modify current vaccines to target the Omicron variant.
Germany's BioNTech and US drugmaker Pfizer said they expect data "in two weeks at the latest" to show if their jab can be adjusted.
Moderna said it would develop a booster specific to the new variant.
With reporting by SBS News