Imam Samudra, 38, and brothers Amrozi Nurhasyim, 47, and Ali Ghufron, 48, were taken before firing squads in a field near their high-security prison on Nusakambangan island just after midnight, Jasman Panjaitan, a spokesman for the attorney general's office, told reporters.
The men died instantly, he said, adding that their eyes were left uncovered at their request.
The Oct. 12, 2002, attacks - allegedly funded by al-Qaida and carried out by members of the Southeast Asian militant group Jemaah Islamiyah - were the first of several suicide bombings that thrust the world's most populous Muslim nation onto the front lines in the war on terror.
The three men never expressed remorse, saying the blasts were meant to punish the U.S. and its Western allies for alleged atrocities in Afghanistan and elsewhere. They even taunted family members of victims - 88 of whom were Australian - at their trials five years ago.
The executions, which were sensitive for both political and security reasons, ended years of uncertainty about their fate.
Repeated postponements have frustrated survivors and relatives of victims, and enabled the bombers to rally supporters from behind bars by calling for revenge attacks in interviews aired on local television stations or published in newspapers and books.
The bombers' bodies were taken by helicopters to Tenggulun and Serang, their hometowns in east and west Java respectively, where thousands of sympathizers and onlookers turned out Sunday for their funeral processions.
Dozens of radicals scuffled briefly with police in Tenggulun, home of the two brothers, Nurhasyim and Ghufron, but there were no serious disturbances.
Muslim cleric Abu Bakar Bashir, led the prayers for the brothers, one of their final requests.
Former militants and police allege Bashir headed Jemaah Islamiyah in the early 2000s. But while he was found guilty of giving his blessing to the Bali attacks, his conviction was overturned after he spent more than three years in jail.
Bashir said Saturday the bombers had "sacrificed their lives" for "the struggle of Islam."
It was a day of mixed emotions for survivors and relatives of victims in Australia.
Brian Deegan of Adelaide, who lost his son Josh in the bombings, said "the tears don't roll quite as often, that absolute gut-ache has diminished a bit," but that nothing will ever make the pain disappear.
He staunchly opposes capital punishment and worries about revenge attacks, even though Jemaah Islamiyah has been severely weakened by hundreds of arrests, with its last attack occurring more than three years ago.
"There's no shortage around the world of persons that are prepared to commit suicide to achieve a result," Deegan said.
Others expressed relief that justice had been served at last.
"These guys went to set about mass murder and paid the highest penalty," said Peter Hughes of Perth, who suffered horrific burns in the bombings. "It doesn't feel good, but they did do the crime and they've paid for it."
Though the three Bali bombers said they were happy to die as martyrs, their lawyers fought for years to stop their executions, arguing they were convicted retroactively on anti-terrorism laws.
They also opposed death by firing squad, saying their clients preferred beheadings because they were more "humane."
The three men were among more than 30 people convicted in connection with the twin nightclub blasts.
Jemaah Islamiyah was blamed for at least three other suicide bombings in Indonesia, but the 2002 attack was by far the bloodiest.
One of the attackers walked into Paddy's nightclub on a busy Saturday night, setting off a bomb attached to his vest. Minutes later, a larger car bomb exploded outside the nearby Sari Club.
The dead included 38 Indonesians, 28 Britons and seven Americans - most revelers fleeing the first blast.
Dozens of victims and tourists gathered at "ground zero" of the bombings Sunday to pray and pay their respects to the dead.
Associated Press writers Zakki Hakim, Ali Kotarumalos and Niniek Karmini in Serang and Jakarta, and Tanalee Smith in Sydney contributed to this report.