Thousands of police officers have taken up positions around the courtroom on Thursday as Bashir, who allegedly heads the Jemaah Islamia (JI), could face up to eight years in jail if found guilty.
But the ruling, which could see a much lighter sentence or even an acquittal, may disappoint those who regard Bashir as an al-Qaida-linked kingpin.
The trial, which began in October last year, is the second time Indonesian prosecutors have gone after Bashir.
The first effort to convict him of leading JI using laws against subversion was thrown out by judges because of lack of evidence.
Bashir, did, however serve 18 months for immigration offences and was released last April, only to be immediately re-arrested on new charges.
The latest trial too has been plagued by weak evidence and reluctant witnesses, although some analysts say there is a case.
"I don’t think people should rush to assume that he will be acquitted," said Timothy Lindsey, director of the Asian Law Centre at the University of Melbourne and an expert on Indonesia.
However, the inability of prosecutors to gain a conviction in the first case on the more serious counts reinforced the view of many Indonesians that Jemaah Islamia does not exist, and that the war on terrorism was a US effort to oppress Islam.
Bashir has been charged with criminal acts of arson and explosion in relation to 2002 blasts on Bali island that killed 202 people and the bombing of a Jakarta hotel in 2003 that killed 12.
He has denied all the charges as well as the existence of Jemaah Islamia.