According to police, Abu Dujana, 37, speaks fluent Arabic, is a skilled bomb-maker and used at least six aliases.
He is also said to have met Osama bin Laden, the leader of the al-Qaeda network, while training in Afghanistan.
Abu Dujana was arrested on Saturday in one of a series of raids that netted seven other suspects. His identity was confirmed after DNA tests and fingerprinting.
Police believe he had close ties with Noordin who appeared on a video in late 2005 threatening attacks against the US and its allies in the war on terror.
Noordin is allegedly one of JI's chief recruiters and has successfully evaded Indonesian authorities for years.
In the video Noordin claimed to be head of "al-Qaeda's Jihad Organization in the Malay Archipelago", a previously unheard of group.
"We will continue the search [for him] until we are successful," said police spokesman Sisno Adiwinoto.
Indonesia's anti-terror police, backed by intelligence officials from the US and Australia, have arrested about 300 terror suspects in recent years, of whom 200 have been successfully prosecuted.
Police were also focusing on three Indonesian-born suspects – named as Zulkarnaen, Dulmatin and Umar Patek – all of whom are wanted for their alleged roles in the 2002 Bali bombings.