The 46-year-old woman and her 24-year-old son were found stranded on Balaloho Island, one of the small inhabited islands in Selayar, by fishermen, officials said.
More than 200 rescuers aboard vessels were joined by Indonesian troops, police, fishermen and residents, said Andi Sultan, head of emergency response in Makassar.
"Rescue teams also faced extremely harsh weather conditions, including waves as high as 2–3 meters and strong winds," Sultan said.
Search and rescue team retrieved five survivors on Saturday evening, including a seven-year-old girl, who were clinging to a fish trap.
They were taken to the port in Benteng town for health checks.
At least one person was confirmed dead.
The KM Nurul Salsa, which was carrying 78 passengers and crew, experienced engine failure and sank Wednesday about 79 kilometres from the port in the Selayar Islands, in South Sulawesi Province.
Passenger boats are a common form of transportation in Indonesia, an archipelago with more than 17,000 islands.
Lax safety standards and problems with overcrowding frequently result in accidents.
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