Janjalani is believed to have been killed in a clash with soldiers on southern Jolo Island on September 4, about a month after the military launched an offensive there
The news came four days after US-backed Philippine troops killed Abu Sulaiman, a senior Abu Sayyaf commander, marking a victory in a US-backed campaign to wipe out Islamic fighters in the south of the archipelago after years of bombings and kidnappings.
Janjalani's death was confirmed after DNA tests carried out by the FBI compared tissue samples taken from remains found buried in the jungles of southern Jolo island in December with those of Janjalani's brother, Hector, who is serving prison time, military chief of staff general, Hermogenes Esperon, said Saturday.
"The Armed Forces of the Philippines is proud to announce that we have neutralised the centre of gravity of terrorism in the Philippines," Esperon said in a news conference.
DNA samples from Janjalani were compared with those of his brother, Hector, who is serving prison time, he said.
Janjalani had been arrested but escaped from a detention cell at the national police headquarters in 1995.
He took over as Abu Sayyaf chieftain after his elder brother, group founder Abdurajak Abubakar Janjalani, was killed in 1998.
US-backed Philippine troops launched "Oplan Ultimatum" on August 1 on Jolo Island, about 950Km south of Manila, targeting Janjalani and other Abu Sayyaf leaders including top Indonesian suspects Dulmatin and Umar Patek.
Dulmatin and Patek are blamed for the October 2002 bombings in Bali, Indonesia, that killed 202 people.
They are also accused of being responsible for training Indonesian and Filipino Muslim fighters on bomb-making techniques.
Janjalani and his key commanders have been charged with several deadly attacks in the Philippines, including a 2004 ferry bombing which killed 116 people in one of Southeast Asia's worst terrorist atrocities.
They are also believed to have carried out mass kidnappings, including the seizure of dozens of students and teachers on the southern island province of Basilan in 2000, and the abduction of 17 Filipinos and three American tourists including the missionary couple Martin and Gracia Burnham and Guillermo Sobero from an island resort in May 2001.
Philippine troops and Abu Sayyaf gunmen clashed on Jolo Island on Tuesday and troops recovered the body of one of the militants, who was confirmed by the military the following day as Abu Sulaiman.
Sulaiman, an engineer whose real name is Jainal Antel Sali Junior, is believed to be one of two possible successors of Janjalani. He also carries a US$5m bounty offered by Washington.
Sulaiman allegedly masterminded attacks and kidnappings in the Philippines, including the 2001 resort raid, the 2004 ferry bombing, and near simultaneous bombings in Manila and two southern cities on last year that killed at least eight people and injured dozens of others.
The deaths of Janjalani and Sulaiman leave Radulan Sahiron, Isnilon Hapilon and Abu Pula among the senior Abu Sayyaf veterans still active, along with about 400 follower.