On Thursday, Bashir was cleared of terrorism allegations but was jailed by a five-member panel of judges after being found guilty of involvement in a "sinister conspiracy" behind the 2002 Bali bombings which killed 202 people.
"The panel of judges decided that the defendant, Abu Bakr Bashir, has been legally and convincingly proven of engaging in a sinister conspiracy that led to fire and the death of others," Chief Judge Sudarto said.
The judges said Bashir's words to key Bali bomber Amrozi and Hutomo Pamungkas during a meeting in Solo, Central Java, in 2002, had constituted a conspiracy.
Bashir had told them "I leave it up to you" when he was notified by Amrozi that he and his friends were planning "a programme" in Bali.
The verdict was greeted by shouts of "Allahu akbar (God is greatest)" by his followers inside and outside the court room. The judges were immediately whisked out of the room by police.
More than 800 police officers were deployed around the agriculture ministry complex in south Jakarta where the trial was being held.
Charges that Bashir had planned
the Bali bombing were dropped
It is the second time the man accused of leading the alleged Southeast Asian arm of al-Qaida, Jemaah Islamiya, has faced terrorism charges.
The white-bearded Bashir, 66, looked frail in court, dressed in his traditional white robe and shawl, a white skullcap and glasses.
Prosecutors had demanded an eight-year prison sentence for Bashir for failing to prevent Jemaah Islamiya members from carrying out attacks.
The main charge that Bashir and his supporters planned the Bali bombings and the bombing of the JW Marriott hotel in Jakarta in 2003 had been dropped for lack of evidence.
Prosecutors in their indictment said that as Jemaah Islamiya chief, Bashir visited one of its training camps in the Philippines in 2000 and allegedly relayed a "ruling from Usama bin Ladin which permitted attacks and killings of Americans and their allies".
Indonesia has come under pressure from the United States and Australia to act against Bashir, and the trial has heard evidence that Indonesia was asked to hand him over to the US authorities.
"If Allah decides that I remain in detention, if the judges do not free me, we should also not react excessively"
Abu Bakr Bashir
Shortly before Thursday's court session, Bashir said if he was found guilty it would be a "tyrannical verdict", but he appealed to his followers not to react with violence if he was convicted.
"If Allah decides to free me, then we should not be overly happy but if Allah decides that I remain in detention, if the judges do not free me, we should also not react excessively," Bashir said.
Bashir maintained that US President George Bush, "the enemy of Allah", had pressured Indonesia to jail him to stop him campaigning for Islamic law.
Bashir was arrested a week after the October 2002 Bali bombings and was first put on trial the following year.
Jemaah Islamiya has been blamed for a series of attacks in the region, including a bombing outside the Australian embassy in Jakarta last September that killed 11 people.