In a statement last month, the ship's line, Holland America, said the cruise would end in Australia as a result of the coronavirus pandemic and that passengers would have to disembark in Fremantle on March 22.
It said requests by several passengers to travel on board to the final destination, Fort Lauderdale, were denied, as it was unsafe as most of the ports along the route were not accepting cruise ships.
On Thursday the Queen Mary 2 passenger vessel departed from Durban after six South Africans disembarked.
The vessel was allowed the enter the port on Tuesday after crew were tested for Covid-19.