Indonesia's most-wanted terrorist, Santoso, was with four other militants, including two women, one of whom was his wife, when he was killed in a firefight with troops on Monday.
The leader of the East Indonesia Mujahideen, or Mujahideen Indonesia Timur (MIT) as it is known locally, was shot dead alongside one other militant in Tambarana village in Poso, in Central Sulawesi.
Police said the pair were killed beside a river and a rifle was recovered. The others managed to escape.
A mole on the forehead of one of the bodies led police to suspect that it could be Santoso, 39, but they waited a day for identification tests to confirm it was indeed the terrorist.
Another clue was the M-16 assault rifle recovered at the scene. Santoso had been known to carry a similar rifle.
National Police Chief Tito Karnavian told reporters that his officers who had previous encounters with the militant, as well as local residents who knew him, were sure it was the MIT leader.
"It's definitely Santoso," said Central Sulawesi provincial police chief Rudy Sufahriadi, after tests to identify the body were completed.
"I have hunted him and I have arrested him before, we have asked people and we have sent people who fought against him (to identify the body)... They have confirmed it was him," he told AFP.
Some of the forensic tests included comparing DNA samples with blood drawn from a child fathered by Santoso, as well as getting five of his followers, who were recently arrested and now serving time in jail, to identify the body.
Santoso and his men from the MIT had pledged allegiance to the Islamic State in Iraq and Syria two years ago and were behind numerous attacks on the police since 2012.
In March, the United States imposed a special terrorist designation on Santoso, blocking any US assets he might have, banning dealings with him by Americans and opening the way for US law enforcement action against him.
Following a series of terror attacks, starting with the 2002 Bali bombings, Indonesia mounted a crackdown on domestic militant cells, eventually dismantling the old Jemaah Islamiah network.
Santoso and other MIT members, however, remained elusive even after a massive manhunt was launched to hunt them down.
Counter-terrorism experts, while welcoming his demise, said that it would not end Indonesia's war on extremism.
Institute for International Peace Building director Taufik Andrie told The Straits Times that it was an achievement for the police and military. "But it does not mean the MIT and other groups will be disbanded," he added.
Coordinating Minister for Political, Legal and Security Affairs Luhut Pandjaitan has said that even though Santoso had been killed, Indonesian security forces involved in Operation Tinombala - the kill-or-capture mission against Santoso's group - would continue going after the remaining MIT members.
"There are up to 19 others," he said, adding that troops on the ground would be reinforced to pursue the other militants still at large.
General Tito also urged those still at large to come out from their hideouts and end their terrorist acts.
"They (must) leave their hideouts and undergo legal process," the police chief said at the State Palace.
More than 3,000 security personnel, including from the military and the police, have been involved in the operation against Santoso since January this year.