After years of hunting for him, Indonesian police caught up with Noordin in Solo, Central Java, on Sept. 17. He was one of four militant suspects killed in a lengthy siege.
Regional leaders say Noordin's death could help undermine militant activities throughout Southeast Asia.
Noordin, 41, has been blamed for a string of terrorist attacks in Indonesia, where al-Qaida-funded suicide bombings have killed more than 250 people, most of them foreign tourists on the popular resort island of Bali, since 2002.
He left Malaysia in late 2001. He was accused of leading a splinter group of the al-Qaida-linked Southeast Asian militant network Jemaah Islamiyah.
Indonesian authorities handed over Noordin's body to his Malaysian-based wife and brother, who flew it back to Kuala Lumpur on Friday and returned to Noordin's home village in Malaysia's southern Pontian district.
Several hundred people watched as the body was taken into a mosque for ceremonial rites just before dusk.
Family members, some with tears brimming in their eyes, hugged each other and shouted "Allahu Akbar," or "God is great" as Noordin's body was lowered into a grave near those of his parents and a dead brother. Police sealed off part of the cemetery to allow only Noordin's relatives near the grave.
"It's been so long since we've seen him. We don't know what to say. We never expected it to be like this," said one of Noordin's nephews, who asked not to be identified because he didn't want his employers in Kuala Lumpur to know he was related to Noordin.