The plane with 112 passengers, including 96 Australians, was boarded immediately after arrival by medical staff in hazmat suits. Thirteen of 16 New Zealanders were transferred to a charter flight home.
The operator of the Greg Mortimer, Aurora Expeditions, confirmed this week that 128 of 217 passengers have tested positive for the coronavirus. Uruguay foreign minister Ernesto Talvi said two Australian passengers remain in intensive care in a Montevideo hospital.
The ship was stranded in Uruguay for more than two weeks after leaving Argentina on March 15 for a 16-day return trip to Antarctica.
"Everybody who needs to go to hospital will go to hospital and the remaining passengers will go into quarantine in hotels," said Victoria state Deputy Chief Health Officer Dr. Annaliese van Diemen.
The returning New Zealanders will also be quarantined in hotels.
"As a large proportion of passengers on the Greg Mortimer have tested positive for COVID-19, all passengers are being treated as though they are COVID-positive as a precautionary measure," a foreign ministry spokesperson said.
Meanwhile, South Australia state reported the death in Adelaide Hospital on Sunday of a 74-year-old man who contracted the coronavirus aboard the cruise ship Ruby Princess.
More than a dozen Ruby Princess passengers have died from the virus and more than 500 people have been infected.
Australia's national death toll stands at 57.