Prime minister Scott Morrison said Sunday the cricketers had not been given any special treatment, and would be coming back "under their own steam, on their own ticket".
They are now expected to undergo 14 days of quarantine in a Sydney hotel, as part of strict border controls that have largely contained the spread of the virus in Australia.
Adam Zampa, Andrew Tye and Kane Richardson had left their IPL teams ahead of the larger Australian contingent, and were due to have completed quarantine last week.
The IPL started in early April with the decision to go ahead in the face of a deepening health crisis prompting criticism from some observers, while others defended it as a welcome distraction for the embattled Indian public.
India reported more than 310,000 new infections and 4,000 deaths on Sunday, with the official number of Covid fatalities in the nation of 1.3 billion people now exceeding 250,000.