There were no official comments on the physical condition of the two who were snatched from their fishing vessel in the waters between the southern Philippines and Malaysia in November 2016, a police statement said.
The two were reportedly turned over by a "concerned citizen" late Thursday to a former governor on the southern island of Jolo, a longtime haunt of the Abu Sayyaf extremist group, some of whose members have pledged allegiance to Daesh, the statement added.
The ex-governor called the police who picked up the two. Officials would not say if ransom, a frequent motive for such abductions, was paid in this case.
The Abu Sayyaf is a loose network of militants formed in the 1990s with seed money from Osama bin Laden's Al-Qaeda network, and has earned millions of dollars from banditry and kidnappings-for-ransom, often targetting foreigners.
The group is based in the strife-torn southern islands like Jolo but its members have sometimes crossed the southern maritime borders to carry out attacks in Malaysia.
This has prompted Malaysia and Indonesia to join forces with the Philippines in boosting its sea patrols in the area.
Indonesian embassy officials could not be contacted for comment.
Abu Sayyaf members were among the Muslim armed groups who rampaged through the southern city of Marawi in May, resulting in a five-month long battle that left more than a thousand dead.
In another incident in the southern Philippines, about 10 extremists clashed with soldiers before dawn Saturday, the military said.
There was no confirmation of casualties on either side but troops later recovered grenades, rockets and a black Daesh flag.