In delivering the sentence, judges said the suspect Mubarok was guilty of a "crime against humanity" for his role in the attack on Western holidaymakers on 12 October, 2002.
Mubarok is the fifth suspect to be sentenced, after three others were earlier sentenced to death and one was given life imprisonment.
Mubarok, alias Hutomo Pamungkas is a self-confessed member of the Jemaah Islamiyah group that has been blamed for the blasts.
Chief judge Nengah Suryadi said the bombings were an "extraordinary crime."
He said Mubarok also admitted bringing weapons to Ambon in eastern Indonesia, the scene of bloody Muslim-Christian strife earlier this decade.
The judge said Mubarok was also directly involved in a church bombing in Mojoketro in East Java, one of a series of church bombings that rocked the country on eve of Christmas in 2000, killing 19 people.
But the judge said Mubarok, 33, had been respectful throughout the trial, had confessed his crime and had expressed regret.
Sporting a shirt and clean-shaven, Mubarok heard the verdict silently. His lawyer said he would consider whether to appeal.