This is the first case of the variant which is thought to be highly transmissible that has been confirmed in Ireland.
There had been at least 14 suspected cases of the virus isolated and eight sent for whole genome sequencing in recent days, following a trawl of positive samples at the National Virus Reference Laboratory once the new variant was discovered.
"There is one case. We thought there would be more," they said in a technical briefing today.
Enhanced contract tracing is underway.
The case involves recent travel to one of the southern African countries and was linked to a positive case last week.
The suspected cases were identified by an S-gene dropout characteristic which it exhibits, but the dominant variant in Ireland, Delta, does not. This trait can be spotted by standard PCR tests.
Cases of Omicron identified in Nigeria have also dated as far back as October, suggesting the variant may have been far more widespread than previously thought earlier in the year.
The concern around the variant from within the scientific community stems from the number of mutations it exhibits on its spike protein, the part of the virus that binds to human cells and infects people.
The spike protein of Omicron is sufficiently different to previous strains that scientists have cause for concern it may be more transmissible than previous strains of Covid-19 but may also evade the antibody response produced by the immune system and vaccines.
There is still much work to be done on this variant to confirm if it is more transmissible or whether it has vaccine-escaping properties, though, the scientific community has cautioned.
Most of the reported cases of Omicron have been either mild or asymptomatic but a caveat to this is they are mostly among young people or people who are fully vaccinated, where cases would tend to be mild.
There have been hospitalisations due to the variant in South Africa, Dr Angelique Coetzee confirmed in recent days.
Any arrivals into Ireland will now have to produce a PCR test 72 hours before travel or an antigen test 48 hours before travel in a bid to slow the spread of the variant in Ireland. This antigen test must be professionally conducted and cannot be a self-test purchased in a store.