Police said they would ask members of Noordin's family to provide a DNA sample for comparison.
Step Vaessen, Al Jazeera's correspondent in Jakarta, said: "In the last few hours we saw an increase in violence at the house; a lot of shooting; a lot of explosions, so it was really hard to imagine that there was someone still alive in the house.
"Five police officers went inside the house - we heard shots from inside the house - and then they came out in a very cheerful mood, giving each other high-fives, showing that the whole thing was finished."
Police reportedly surrounded the house at 4pm (09:00GMT) on Friday after arresting two people at a nearby market who were said to be relatives of the tenant of the property.
Sidney Jones of the International Crisis Group said that Noordin's apparent death followed the arrest of another key suspect shortly before the Jakarta bombings.
"There was a man arrested in late June that I think must have been part of the original plotters and was certainly part of his network," she told Al Jazeera from Jakarta.
"From his information and some of the leads gathered after the hotel bombings they must have had enough to trace Noordin to where he was hiding.
"Now its a case of rounding up other people in the network and what we don't know is whether we are dealing with 20, 40 or 50 people."
Noordin is the Malaysian-born head of an Islamist splinter group with connections to Jemaah Islamiyah, a group fighting for an Islamic state in southeast Asia.
Karim Raslan, an Indonesian political commentator, told Al Jazeera that the killing of Noording would be a "very significant coup".
"However, I think that many people will still be concerned as to the extent to which Noordin Top has actually managed to move his group throughout southeast Asia," he said.
As well as having been blamed for the Jakarta attacks, Noordin is believed to have played a major role in four other bombings in Indonesia since 2002, including the nightclub bombings on the resort island of Bali that year that killed 202 people.
In a video in 2005, the Malaysian citizen claimed to be al-Qaeda's representative in Southeast Asia and to be carrying out attacks on Western civilians to avenge Muslim deaths in Afghanistan.
Also on Saturday, Indonesian police killed two suspected Islamic fighters and seized up to 500kg of bomb-making material after a raid on a house in Bekasi, near Jakarta, police said.
Bambang Hendarso Danuri, the national police chief, said that the raid was linked to the operation in Central Java and targeted a "cell of NMT," referring to Noordin.
|Police said two other suspects were killed in a raid on a house in Bekasi near Jakarta [AFP]
"We had to shoot them because at the time of the raid they had hand-held bombs that were about to be thrown at the police," he said.
"They were would-be bridegrooms [suicide bombers] with special targets for attacks to be carried out two weeks from now."
Al Jazeera's Step Vaessen said: "Two bombs have been found, which, according to police sources, were going to be used to bomb the president's house not far from where they were found."
Nanan Soekarna, the national police spokesman, identified the two suicide bombers as a 19 year-old man and 28 year-old man who carried out deadly attacks on the Jakarta hotels last month.
The July 17 attacks on the Marriott and Ritz-Carlton hotels killed nine people and wounded 53 others, including Indonesians and foreigners.
The bombings broke a four-year lull during which there had been no major attacks.