NSW Health said the fully vaccinated traveller who recently visited southern Africa tested positive to the variant.
The man arrived on flight QR908 from Doha to Sydney on November 25 and tested positive to COVID-19 yesterday.
The man arrived on the same flight as the Central Coast woman who tested positive to Omicron yesterday.
NSW Health has issued an exposure site alert which was visited by the man.
Anyone who attended the Chemist Warehouse, The Grove in Liverpool on Monday November 29 between 8.10pm and 8.15pm is now deemed a close contact.
If you attended the venue at that time you must immediately get tested and isolate until a negative result is received.
The man had spent the last six months in Nigeria, which is not one of the eight African countries subject to the border closure issued on Saturday.
It is not yet known whether he contracted the virus in Nigeria or while on the flight from Doha.
NSW Health Minister Brad Hazzard said he believes the man only has mild symptoms.
“We’re hoping that stays the case,” he said.
“And I thank him for coming forward and being tested.”
Further testing today should confirm whether he does have the Omicron strain.
All passengers on the QR908 Qatar Airways flight have been directed to get tested and self-isolate for 14 days.
So far, only one of the seven Omicron cases in Australia are not in New South Wales.
The seventh is a case in quarantine in Howard Springs in the Northern Territory.
Mr Hazzard said he is “not keen to see a return to lockdowns”.
“As one who has delivered that news, bad news to the community on many occasions, I feel like it’s time for a change in approach,” he said.
“We don’t know how many more variants of this virus are going to come.”