Rescuers called off the hunt for the remaining passengers on Tuesday, almost three months after Flight QZ8501 went down in stormy weather as it flew from the Indonesian city of Surabaya to Singapore, killing all 162 people on board.
The crash of the Airbus A320-200 sparked a huge international search, with ships and aircraft from several nations scouring the waters for the plane wreckage and the victims.
In recent weeks the hunt had already been scaled back, with just Indonesia's civilian search and rescue agency involved and only a small number of new bodies found.
Early Wednesday, the last ships involved in the search left Pangkalan Bun, the town on Borneo island which had served as a base for the hunt, said agency official S.B. Supriyadi.
A total of 106 bodies have been recovered, with the last three found at the weekend.
Hadi Widjaja, whose son and daughter-in-law were on the flight, praised rescuers for doing a "good job".
His son has been found but his daughter-in-law remains missing. He said her family realised it was time to move on.
"Her parents and my family have let her go in peace. We have to accept this sad reality," he told AFP.
"The rescuers spent three months on this search operation," he said, adding that his family "really appreciated their work".