The killing of Dulmatin, who had a 10-million-dollar bounty on his head, marked another coup for Indonesian authorities in the fight against Islamist militants blamed for a series of deadly attacks in recent years.
Last year, police killed Noordin Mohammad Top, a Malaysian-born militant who allegedly played major roles in bombings in Indonesia since 2003, including the twin hotel attacks in Jakarta last year.
"DNA samples taken from his mother and 12-year-old son matched," said Brig. Gen. Mussadeq, head of the national police's medical center.
Anti-terrorism police raided an internet cafe in a southern Jakarta suburb and killed a man believed to be Dulmatin, whose real name was Joko Pitono.
President Susilo Bambang Yudhoyono earlier Wednesday announced in Australia, where he is on an official visit, that he had received confirmation that the man was Dulmatin.
National police chief Bambang Hendarso Danuri said the other two men killed in a separate raid in the same area Tuesday were Dulmatin's guards, identified as Ridwan and Hasan Nur.
He said two suspects were also arrested Tuesday and another two Sunday.
Police also found three detonators for use in remote-controlled bombs, a revolver and a handgun in Tuesday's raids, Danuri said.
Dulmatin, a 39-year-old Indonesian said to be a member of the Jemaah Islamiyah regional militant group, was believed to have fled to the Philippines after the Bali bombings, in which 202 people were killed.
In 2005, the United States offered a 10-million-dollar reward for Dulmatin's capture.
Philippine authorities twice thought that Dulmatin had been killed in military operations on the southern island of Mindanao.
Tuesday's raids came after a major operation targeting suspected Jemaah Islamiyah militants in the westernmost province of Aceh, and less than two weeks ahead of a visit by US President Barack Obama to Indonesia, scheduled for March 20-22.
Danuri said 18 suspects were arrested and three others were killed in the operation in Aceh, while the police lost three officers.
Metro TV news channel broadcast a video that it said showed people armed with rifles conducting military training in Aceh. A man was seen in the video delivering a sermon.
Police said militants operating in Aceh had no ties with the Free Aceh Movement, a separatist group that in the past had fought for an independent state in the province.
They said insurgents were setting up a base in Aceh to plan terrorist attacks and create chaos to destabilize the country.
Aceh was the scene of a long separatist insurgency until a peace pact was signed between the rebels and government in 2005.
The pact followed the December 2004 Indian Ocean tsunami, which left about 170,000 people dead in the predominantly Muslim province.
