Mukhlas, whose real name is Ali Ghufron, was executed in 2008 along with two others already convicted over the attacks, Amrozi and Imam Samudra.
Patek told the court he did not know the exact locations of where the devices would be detonated.
The Sari Club was bustling with locals and tourists when a massive bomb loaded into a van parked outside was detonated just after 11pm on October 12, 2002.
About 20 seconds earlier, a suicide bomber had detonated a backpack loaded with explosives inside Paddy's Bar.
"I was very sad and regret the incident happened, because I was against it from the start. I never agreed with their methods," Patek said.
"I didn't know which targets would be bombed."
He also repeated a claim initially made shortly after his extradition to Indonesia last year that he had made an 11th hour bid to convince members of the Jemaah Islamiah (JI) terror cell responsible for the bombings to call off the attack.
The 45-year-old claimed he told other members of the group that the amount of explosives being used would kill many people, "including Muslims", and that they should abort the plan.
Asked by the judge why he didn't just leave, Patek said he had only 10,000 rupiah (NZD$1.40) in his pocket.
Patek was captured in January last year in the Pakistani town of Abbottabad, where US forces killed al-Qaeda leader Osama bin Laden less than four months later.
Earlier in the trial, FBI agent Frank Pellegrino said intelligence gathered during the interrogation of another terrorism suspect known to Patek confirmed the 45-year old had travelled to Pakistan in an effort to meet with bin Laden.
But Patek told the court no meeting ever took place. He also claimed he had no idea that money used to finance the bombings almost a decade before he travelled to Pakistan, had come directly from bin Laden.
"In God's name, I never met Osama bin Laden. I knew nothing about where the funding came from," he said.
Patek is suspected of having been involved in terrorist activities since the early 90s after being trained to make explosives at a Mujahideen camp on the border of Pakistan and Afghanistan.
It's believed that between 1996 and 1998 he was involved with the Moro Islamic Liberation Front in the Philippines, before returning to Indonesia and linking up with JI.
He fled back to the Philippines following the 2002 Bali bombings, after which he spent almost 10 years at the top of South-East Asia's most wanted list before his capture and extradition to Indonesia last year.
- AAP