Health Minister Martin Foley confirmed the man, from Melbourne's eastern suburbs, tested positive on Friday morning.
The man, who is asymptomatic, arrived in Melbourne on Wednesday after completing 14 days of quarantine at Perth's Mercure Hotel.
Genomic testing has confirmed the virus spread in the corridors of the hotel, from a couple who had returned from India.
The man was staying in the room adjacent to the couple, Mr Foley said.
The man was picked up from Melbourne Airport on Wednesday by his spouse and returned home. He has only come into contact with his spouse and their two children, who were tested on Friday morning.
Mr Foley said the man has requested to be moved to The Holiday Inn on Flinders Street, which functions as a 'health hotel' for international arrivals with COVID-19.
Everyone on Qantas flight QF778 from Perth to Melbourne on Wednesday will be contacted by the Victorian public health team and required to isolate for 14 days.
"We will be examining the gentleman's movements, particularly through the airport, where he did wear a mask, as he did on the flight," Mr Foley said.
The man will be included in Victoria's COVID-19 figures on Saturday, bringing to an end the state's 56-day run no locally acquired community transmission.
"This is an important and timely reminder to all of us that this global pandemic is not over," Mr Foley said, urging eligible Victorians to get vaccinated.
WA Premier Mark McGowan on Thursday announced the Mercure would no longer accommodate returned overseas travellers.