The blasts, which came just over a year after the 9/11 attacks on the United States, ripped through two bars packed with foreign tourists, and remain the deadliest militant assault in Indonesia’s history.
Zulkarnaen, a high-ranking member of the Jemaah Islamiyah (JI) militant group, was on trial for the Bali bombings as well as several other attacks carried out by a special unit under his command.
He “is guilty of committing terrorism and is sentenced to 15 years behind bars”, said the presiding judge at East Jakarta District Court.
The 58-year-old Zulkarnaen, whose real name was listed with the court as Arif Sunarso, was on Indonesia’s most-wanted list since the bombings, and evaded the authorities for nearly two decades until his arrest in Dec 2020.
Indonesian prosecutors had said Zulkarnaen set up the special JI cell and described him as a “key asset” for the group because of his experience as a trainer at militant camps in Afghanistan and the Philippines.
During the trial, Zulkarnaen denied involvement in the Bali bombings, but admitted they were carried out by his team.
He told the court that JI operatives did not tell him about the attack in advance and that he was not involved in specific planning.
But the judges were not convinced.
“The fact that he was the head of the team and agreed on a plan in Bali... it could be considered agreeing to the plan,” the presiding judge said.
The court also flagged other attacks by Zulkarnaen’s cell during the sentencing, including a 2000 attack on the Philippines embassy, as well as a series of church bombings.
His unit was also tasked with inciting ethnic and religious violence in Sulawesi and Molucca islands, where thousands died between 1998 and 2002, according to the police.
Zulkarnaen appeared in court via video link because of coronavirus rules.
Zulkarnaen was among the top leaders of JI, which was founded by Indonesian militants exiled in Malaysia in the 1980s.
The group grew to include cells across Southeast Asia, and developed links with international Islamist groups too.
It has been designated a foreign terrorist group by several nations, including the United States and Australia - which lost 88 nationals in the Bali bombings.
“JI has a common ideology with Al-Qaida and many members of the two organizations have a shared experience of training or fighting in Pakistan and Afghanistan during the late 1980s and early 1990s,” according to a UN Security Council sanctions entry on the group.
Zulkarnaen was one of Al-Qaeda’s “point men in Southeast Asia” and “one of the few people in Indonesia who have direct contact” with the group, according to the US State Department’s Rewards for Justice programme, which offered a bounty of up to US$5 million (B16.5mn) for him.
JI was nearly dismantled by Indonesian authorities after the Bali bombings, but the organisation has been rebuilding.
Its spiritual leader, the firebrand preacher Abu Bakar Bashir, was released from prison last year after serving a jail term for helping fund militant training.
Indonesia has suffered numerous terror attacks since the Bali bombings, and is home to dozens of extremist organisations - including some loyal to the Islamic State (IS) group.