Concluding one in a series of JI cases on Wednesday, Judge Ari Supraptman showed no hesitation in passing judgment on Zaenal Abidin – alias Sarjiyo – despite his demands for a retrial.
Sarjiyo helped make the bomb which devastated the crowded Sari Club on 12 October 2002, killing more than two hundred.
He is only the third man to receive a life sentence for the attack as the three other suspects tried so far have all been sentenced to death.
As the judge banged the gavel, Sarjiyo shouted out his intention to appeal the verdict and protested his innocence.
Although the defendant did not plant the bomb, the court ruled he had helped plan the attack, took part in mixing chemicals and packed explosive powder into filing cabinets which were installed in the back of a van.
The first blast ripped through Paddy's Pub. But it was the second bomb - just seconds later at the Sari Club in the Kuta tourist strip - that claimed most lives.
Sarjiyo had told the court the attack was intended to show that Indonesia could resist what he called a foreign conspiracy to break up the country.
"The objective of our action is to show foreigners that there is resistance in Indonesia. We resist to prevent Indonesia from breaking up," he said last month.
He cited Christian-Muslim fighting in Poso on Sulawesi island and in the Maluku islands and the independence of mainly Christian East Timor as proof of a foreign plot to dismember the country.
Sarjiyo also told the court last month he was in the southern Philippines between 1994 and 1996 to "help Moro jihad fighters".
"The objective of our action is to show foreigners that there is resistance in Indonesia. We resist to prevent Indonesia from breaking up"
Convicted JI bombmaker
There have been several reports that JI fighters have trained and are still training at camps of the Moro Islamic Liberation Front. But the Philippine group denies cooperating with JI.
At another separate trial, prosecutors recommended judges sentence Achmad Roichan - alias Saad - to 20 years in jail.
He is accused of helping to hide key bomber Mukhlas while he was on the run.
Mukhlas, already sentenced to death, was hidden in a small home factory owned by Roichan in the city of Solo. The factory owner will present his defence plea when his trial resumes on 12 February.
More arrests to come
Witnesses have said the Sari Club bomb was built under the supervision of two men who are still on the run - a Malaysian called Azahari Husin and an Indonesian called Dulmatin.
Police have arrested 35 people for the Bali blasts and most have been put on trial and sentenced.
Apart from the Bali attacks, JI is blamed for the Marriott hotel blast in Jakarta in August last year that killed 12 people and a string of other attacks. It aims to create an Islamic theocracy across much of Southeast Asia.