Non-citizens who have been in southern Africa will be banned from entering Australia until further notice.
Federal health minister Greg Hunt said Australia is in a vastly different position to other countries due to high vaccination rates, but there are immediate actions that need to be taken to protect people.
"Our job here is to make rapid decisions, to keep Australia safe, which is what we've done," Mr Hunt told reporters on Saturday.
"It will be difficult for some families and I respect and apologise. This is about keeping Australia safe and we will continue to do that as necessary."
All flights will be immediately suspended for two weeks from South Africa, Namibia, Zimbabwe, Botswana, Lesotho, Eswatini, the Seychelles, Malawi, and Mozambique.
Mr Hunt says anyone who has already arrived in the country from any of those nine countries must go into immediate self-isolation.
"There are no known cases of the Omicron variant in Australia," he said.
"We've taken precautious action in the past, we've taken early action in the past, we are doing that again.
"The difference is that we now have strong vaccines, we have one of the highest levels of coverage in the world, we have one of the most recently vaccinated populations in the world, and we have strong public health and social measures."
Less than a hundred people who have travelled to southern Africa have entered Australia since international borders opened on 1 November, according to chief medical officer Paul Kelly.
The latest variant, given the name Omicron by the World Health Organisation on Saturday morning, first emerged in Botswana and has been detected in South Africa, Hong Kong, Israel and Belgium.
It has developed 30 mutations so far, double the amount of the Delta variant that sparked a third wave of outbreaks and lockdowns in Australia this year.
About 86 per cent of Australians aged 16 and older are double-dosed, which means between 72 and 73 per cent of the entire population, and 92 per cent of Australians aged 16 and older have received a single dose.
1.5 per cent of the country have received a booster shot.
The federal government is sending letters to every household in the country urging people to get their booster shot six months after becoming double-dosed.
Additional reporting by Rayane Tamer.