Some 29 people who had been in one of the nine southern African countries subject to elevated restrictions touched down in Sydney across two flights on Saturday evening.
They have all been sent to hotel quarantine.
All passengers on the Qatar Airways flight are now classified as close contacts and must isolate for 14 days, even if they haven't been in southern Africa.
New South Wales Premier Dominic Perrottet said it's a reminder that the pandemic is not over, and described his approach as precautionary.
However, he cautioned that it must be expected that the variant will spread throughout the world.
"We need to learn to live alongside the virus. We need to learn to live alongside the variants of the virus," he said on Sunday.
Although he's ordered all international arrivals to quarantine at home for 72 hours, Mr Perrottet insisted the NSW international and state borders would remain open.
"We can't be a hermit kingdom on the other side of the world," he said.
"There's only so much governments can do. The best thing we can do as a people is to get vaccinated, get a booster shot, and that will keep you and your family safe."
The three-day quarantine order is on top of a federal government requirement for travellers to enter quarantine for two weeks if they've been in South Africa, Lesotho, Botswana, Zimbabwe, Mozambique, Namibia, Eswatini, Malawi or the Seychelles within the past 14 days.
There are no plans to adjust the state's reopening roadmap, Mr Perrottet said, so restrictions will still ease for the unvaccinated on 15 December.
Omicron testing underway after passengers with COVID-19 arrive in Sydney from Africa
The new variant, named Omicron by the World Health Organisation on Saturday, has been detected in South Africa, Botswana, Hong Kong, Israel, Belgium and the United Kingdom.
It has double the number of mutations as the Delta variant, which sparked a third wave of outbreaks and lockdowns in Australia this year.
Flights from South Africa, Namibia, Zimbabwe, Botswana, Lesotho, Eswatini, the Seychelles, Malawi and Mozambique will cease for two weeks under "precautionary" new federal government measures announced on Saturday.
Non-citizens who have been in those countries aren't allowed into Australia.
Australian citizens and their dependants face mandatory two-week quarantine if they have been in the region.
NSW, Victoria and the ACT will make all overseas arrivals quarantine at home for 72 hours.
People already in the state who have been in the nine countries in the past two weeks must isolate for 14 days and be immediately tested.
Anyone in those jurisdictions who have been to the nine countries in the past 14 days must get a PCR test and quarantine immediately.
In response to Omicron, South Australia extended the length of its quarantine requirement for fully-vaccinated Australian international arrivals to two weeks, and made small changes to its interstate arrival regime.
West Australian Premier Mark McGowan announced SA would be designated "low risk", introducing a quarantine requirement for international arrivals from the state.
He said it was necessary because of quarantine requirements being loosened in recent days.
The changes mean WA is only allowing quarantine-free travel from Tasmania and Queensland. A hard border remains in place for the other state and territories.
Tasmania will bar entry to people who have been in southern Africa unless they have first completed two weeks of supervised quarantine on the mainland.
Commonwealth Chief Medical Officer Paul Kelly said Omicron was spreading quickly, but it wasn't clear that it caused more severe symptoms than existing strains.
It is not yet known whether existing vaccines are any less effective against the new variant than prevailing strains.