Puryanto had his sentence cut by three months, meaning that he had completed his near five-year term in Balikpapan prison on Borneo.
Indonesia traditionally has a prisoner remission programme on August 17, the day it celebrates independence from Dutch colonial rule. Cutting the punishment of anyone involved in the Bali bombings is likely to anger Australia and other countries whose nationals died.
Many of 202 people who died in the bombings were foreign tourists, among them 88 Australians.
The nine prisoners are serving sentences between five and 16 years and were convicted on charges such as robbery to help fund the attacks and giving refuge to people involved in planning them.
Ilham Djaya, Bali's Kerobokan prison governor, said: "They are entitled to remissions because they have behaved well.”
Eight convicts are in prison in Bali and one in Jakarta.
Four people serving life sentences for the Bali bombs were not given remission, he said.
A total of 33 people were jailed over the Bali attacks in 2002.
Among these, Amrozi, Ali Gufron, and Imam Samudra are being held on death row in a jail in Java province for their leading roles in the bombings and are due to be executed this month.
Australia protested against the release in June of Abu Bakar Bashir, a Muslim cleric who served 26 months of a 30-month sentence for conspiracy in the attacks.