Scores of alleged "terrorists" have been arrested or killed in the aftermath of the bombings, including most of Noordin's closest lieutenants.
The operational commander of the attacks, Syaifudin Jaelani, was killed in October.
'Continuing to fight'
The Pakistan-educated suspect, who uses the online moniker of "Prince of Jihad", vowed to fight his conviction.
"I swear I've never met Noordin and God willing I will prove it," he told reporters at court.
"I will continue to fight. If I can't prove that I've never met him in this world, I'm sure it will be proven in the hereafter."
Prosecutors produced an email that Jibril wrote to his brother in the Saudi city of Mecca telling him about a meeting he had had with Noordin a year before the attacks.
In the email, Jibril talked about an operation which would be "bigger than the WTC attack," referring to the World Trade Centre in New York on September 11, 2001.
Meanwhile, in a separate trial, prosecutors sought eight years in jail for a woman for allegedly harbouring Noordin in her central Java home before and after the attacks.
Putri Munawaroh, 20, was the only survivor of the nine-hour shoot-out with police in September in which Noordin and three others, including her husband, were killed.
On Monday, a court cleared Saudi man al-Khelaiw Ali Abdullah, 54, of financing the twin suicide attacks on the hotels.
Muslim-majority Indonesia has been wracked by attacks since 2000, including the 2002 Bali bombings which killed more than 200 people.