They spent about 10 days in the Maldives before the Australian government lifted a temporary ban on citizens who had been in India from travelling home.
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.
Australia head into the Boxing Day clash at the Melbourne Cricket Ground on a high after crushing the visitors by eight wickets inside three days in the opening Test at Adelaide.
All-rounder Cameron Green is guaranteed to make his test debut if he clears concussion protocols but Paine said Green would not be considered for the opening role.
Smith has been repeatedly overlooked in leadership roles in white-ball series this year, though coach Justin Langer admitted there were discussions about him potentially replacing Aaron Finch when the limited overs captain was recently injured.