The ban on travellers is initially set to last 14 days and will come in at midnight tonight.
The newly announced restrictions come just weeks after Israel had reopened to fully vaccinated tourists.
The plans for British families intending to visit Israel over the school holidays will now have been thrown into doubt.
The announcement by Prime Minister Naftali Bennett yesterday made his the first country to shut its borders in response to Omicron.
The government has also authorised the use of phone-tracking technology developed by Shin Bet for counter-terrorism intelligence to locate carriers of the new variant and anyone who has come into contact with them.
The measures were passed at a cabinet meeting yesterday but not without some opposition, with Justice Minister Gideon Sa’ar and Education Minister Yifat Shasha-Biton speaking against the new restrictions.
The new strain was first detected in South Africa and has now been classed as a “variant of concern” by the World Health Organisation (WHO).
Doctors fear that its multiple mutations may enable it to spread more easily than the Delta variant.
There is also concern that it is so different from the original strain of Covid-19 which emerged last year that vaccines may be less effective in preventing infection and stopping severe disease.
It has been detected in countries across the globe. Although cases numbers are currently low they are likely to rise steeply in the coming weeks.
In Israel there has so far been one confirmed case of Omicron.
Officials have yet to reveal whether or not the patient had been vaccinated.
The Health Ministry said yesterday there are a further seven suspected cases, three of whom were fully vaccinated.
Three of the cases had not returned from travel abroad recently, suggesting the variant may already be circulating domestically.
However, there is still limited data on Omicron and its danger to public health.
It is hoped that by the end of the two weeks experts will have more findings enabling them to advise on whether or not it is necessary to continue the ban.
Speaking to Israeli’s television channel N12, Interior Minister Ayelet Shaked said: "Our working hypotheses are that the variant is already in nearly every country and that the vaccine is effective, although we don't yet know to what degree."
Israeli citizens flying back in from abroad will be required to go into quarantine for three days, even if they are already fully vaccinated.
Anyone returning will have to undergo a PCR testing on landing – as is already required – and a second such test 72 hours later.
Should both prove negative they will be released from quarantine.
Travellers who have been vaccinated must stay in quarantine for a minimum of a week, after which if they test negative they are free to go outside.
Returnees from red list countries will have to go into quarantine in an officially controlled hotel until testing negative.
Foreign visitors will be allowed only in exceptional circumstances.
More than 8,000 people in Israel have died from Covid since the start of the pandemic.
The British government has announced a limited set of restrictions in response to Omicron, with a ban of non-UK citizens flying in from a number of countries in Africa along with a new mandate on the wearing of masks on public transport and in shops.
