Media reports had speculated that the seven-months-pregnant Holmes had cancelled her trip at the last minute on the advice of her doctors who had advised against the 14-hour flight.
The couple arrived on Cruise's private jet to show support for Packer's son, James, who has been a close friend of the actor's for five years.
Their friendship grew through the Church of Scientology and Packer has described Cruise as one of "the world's nicest guys".
The celebrity couple accompanied James and his girlfriend, ERICA BAXTER, on a yacht docked outside the Park Hyatt hotel on Sydney Harbour.
Cruise told local media, "It's good to be back in Australia" and that he was "thrilled and excited" about the upcoming birth of his baby.
The MISSION: IMPOSSIBLE star, who is a qualified pilot, admitted he did not fly his private jet to Australia himself, as he was busy working and attending to Holmes.