She replaced him after he was sacked by the national assembly in 2001 amid unproven allegations of corruption and incompetence.
A religious scholar, Abdurrahman was a critic of Suharto but was himself criticised for his erratic leadership style while he was in office.
Still, he gained a reputation for religious tolerance and reformist policies.
He rose to political prominence as leader of one of the country's biggest mass Islamic movements, the moderate Nahdlatul Ulama (NU) and helped put the country on the path to democracy following Suharto's fall.
|Wahid was Indonesia's fourth president [AFP]
Indonesia held its first direct presidential election in 2004, which was won by Susilo Bambang Yudhoyono, who remains president after winning re-election this year.
In a nationally-televised address on Thursday, Yudhoyono called on Indonesians to pay Abdurrahman their "highest respects".
"I say this with prayers and hope that he is accepted at the side of God for his enormous service to the public, the nation and our beloved state," he said.