Budiman Muslimin, 26, and his wife Hasmida Masaniaga, 24, were found clinging on to a single life jacket by a villager off the coast of Pantai Batu Payung at about 6.30pm on Wednesday.
The villager alerted the authorities who launched a search for the remaining 13 people still missing from the boat which had departed illegally from Tawau.
On Thursday morning, six bodies - a man, two women and three children - all believed to be passengers on the boat, were recovered by personnel from the Indonesian National Search and Rescue.
The bodies have been taken to Nunukan in Indonesia for verification.
The seven-metre long boat with 15 people capsized after it was hit by strong waves about 10 minutes after it left Tinagat in Tawau heading towards Sungai Nyamuk in Indonesia at about 6.30pm on Tuesday.
As the boat was illegal, it was only after the discovery of the couple did the authorities became aware of the incident.
A search for the remaining 13 Indonesians – five male adults, three women and five children, including a baby – is underway in an area seven nautical miles south of Tinagat in Tawau waters.
Searchers are also combing for survivors along the coastal areas.
Tawau police chief Asst Comm Fadil Marsus said the search involved personnel and boats from the Malaysian Maritime Enforcement Agency, marine police and firemen.
It was the second boat sinking incident in two weeks in Sabah.
On Jan 28, a boat with 31 people, including 28 Chinese tourists, capsized on its way to Pulau Mengalum from Kota Kinabalu.
Two crewmen and 20 tourists were rescued while four died while a search continues for five more missing.