Umar Patek is accused of being a central figure in the 2002 attacks on two nightclubs on the Indonesian resort island, which killed many Western tourists including 88 Australians.
In an emotional appearance at his trial, Patek, 45, who faces a possible death penalty but says he was only a bit player in the attacks, spoke in a voice cracking with emotion.
"I am taking this opportunity to seek forgiveness from the victims, their families and whoever suffered losses," including the Indonesian government, he said, before repeating the apology to reporters and shaking hands with prosecutors.
"I was very sad and regret the incident happened, because I was against it from the start. I never agreed with their methods," said Patek, wearing a white shirt and trousers that stopped short of his ankles, his hair dyed henna-red in keeping with the Prophet Mohammed's custom.
Patek, who was arrested in the same Pakistani town where Osama bin Laden was killed just months before the Al-Qaeda chief's death, said the attacks on October 12, 2002, had been a "total failure".
He said the plans were drawn up at the home of Dulmatin, another Bali plotter, who was killed by police in 2010.
"The reason was to retaliate the killing of Muslims in Palestine but the people killed had no link to Palestine," he said during his three-hour testimony at the West Jakarta district court.
"Who were the victims, they were Westerners, they weren't Israelis. In fact many Indonesians were victims. They had no link to Palestine," he said, speaking calmly and gesturing with his hands.
When the idea of attacking Bali was brought up, Patek claimed he raised objections.
"I questioned why in Bali? Jihad should be carried out in Palestine instead. But they said they did not know how to get to Palestine," he said, adding: "Dulmatin told me not to think so hard, just help."
Patek allegedly used simple household tools including a rice ladle to assemble the Bali bombs, which according to the court indictment were housed in ordinary filing cabinets.
"The defendant filled up the black powder in four filing cabinets, in the meantime, Dulmatin made the bomb's electronic circuit," the indictment said.
With bombmaker Azahari Husin, a Malaysian later killed at a hideout on Java island, Patek assembled the detonating cord and then loaded the filing cabinets into a car, the document added.
But Patek said Monday his role went no further than mixing the explosives.
"I helped to mix the chemicals," he confessed. "Azahari assembled the bombs. They loaded explosives onto the car while I stayed inside my room and read the Koran."
Patek is accused of being the expert bombmaker for Jemaah Islamiyah (JI), a Southeast Asian terror network linked to Al-Qaeda. He is also accused of attacking churches in Jakarta on Christmas Eve in 2000.
He was arrested in January last year in the Pakistani town of Abbottabad, where US commandos killed bin Laden four months later.
During the trial, evidence has emerged that bin Laden gave JI $30,000 to wage jihad in the region and Patek might have met him when he was in Abbottabad, a claim Patek has repeatedly denied.
"I don't know about the source of funds," he said Monday. "In the name of God, I have never met the man named Osama bin Laden," he added.
US Federal Bureau of Investigation Special Agent Frank Pellegrino testified in April that Patek was widely known as an expert bombmaker.
According to Pellegrino, a witness interviewed by the FBI in the Philippines reported Patek as saying he "was interested in going back to Pakistan and Afghanistan and working with Osama bin Laden".
Patek was once the most-wanted terror suspect in Indonesia and spent nearly a decade on the run with the US offering a $1 million bounty on his head under its rewards for justice programme.
Prosecutors have said they will seek the death sentence on charges of premeditated murder, but will make their formal recommendation on May 21. The verdict is expected June 21.