Earlier reports said Noordin may have been killed during a 16-hour siege with Indonesian anti-terrorism forces at a farmhouse in central Java last Saturday.
According to police Noordin is believed to head an ultra-violent splinter-cell of the Jemaah Islamiyah group, and is the prime suspect in the July bombings.
The twin attacks killed at least nine people and injured more than 50 others.
Noordin has been on the run for years and has a bounty of more than $100,000 on his head for his alleged role in a series of deadly attacks including the Bali bombings in 2002 and 2005.
Announcing the results of the DNA tests on Wednesday, police also released security camera footage that they said showed Ibrohim working at Marriott hotel for at least two years before the July attacks.
Nanan Sukarna, the national police chief, said Ibrohim had worked as "a planner and arranger of the bombings" and that five other suspects in the blasts remain at large, including Noordin.
|Noordin Md Top is high on Indonesia's wanted list over a series of deadly bombings [AFP]
He said Ibrohim began scouting the targets three months in advance and smuggled explosives in through a basement cargo dock a day before the strikes.
The grainy images show a lone man driving a small pick-up truck into the hotel and unloading what police said were three containers of explosives, apparently after skirting all security checks.
Ibrohim was also seen in the video leading the suicide bombers through the hotels on July 8, apparently in a rehearsal for the attacks plotted from two rented safe houses on the outskirts of the capital.
"We know him," Allan Orlob, head of security for the two luxury hotels, told The Associated Press on Wednesday. "He worked as a third-party florist."
Orlob said Ibrohim resigned the morning of the bombings and left only a letter asking for part of his last salary to be used to repay several people who loaned him money.