Friday’s decision ended speculation whether Amrozi bin Nurhasyim, 41, also known as “the laughing bomber” would appeal his conviction of death by firing squad.
"He has signed the letter," Amrozi's chief lawyer Wirawan Adnan said, referring to a document authorising lawyers to appeal against the sentence passed Thursday.
A court in the resort island condemned Amrozi to death for his role in the 12 October bombings which killed 202 people.
Amrozi admitted to purchasing the chemicals used in the blasts and the van, and transported them to Bali.
Adnan said the appeal would be filed on Monday. Defence lawyers could not have appealed the sentence without Amrozi's authorisation.
But earlier on Friday Adnan said Amrozi had told him that he would not seek leniency.
"He believes that his life is not in the hands of judges and that he does not want to be a whiner by asking for their mercy," Adnan said.
"But Amrozi has also told us that he would leave the legal matters to us."
"Amrozi has also told us that he would leave the legal matters to us."
Chief lawyer Wirawan Adnan
Amrozi was the first suspect to face judgement for the bombings, the worst terror attack since 11 September, 2001 in the United States.
In response to his sentence, Amrozi turned to the crowd behind him, smiled broadly and gave two thumbs up in approval.
Local newspapers welcomed the death sentence, with the Jakarta Post describing it as "an event of major significance" in its editorial.
But other newspapers noted Amrozi's reaction to being given the death penalty.
Koran Tempo said the response was a reminder that terrorism cannot be defeated by relying only on heavier penalties and repressive actions.
"Why? Amrozi's thumbs-up drives us to reply that we will never run out of militants ready to become martyrs," the paper wrote in an editorial.
The paper said rising "social frustration" and exploding unemployment contribute to militancy while Megawati's government has failed to promote democratic reform necessary for combating terrorism.