Hasanuddin had faced a maximum sentence of death and said before the verdict that he was ready to face the firing squad.
During his trial Hasanuddin admitted being involved in the killings, but denied masterminding the attacks.
He also asked the families of the schoolgirls for forgiveness.
"We are not cold-blooded killers," he told the central Jakarta district court in November. "We just wanted revenge."
More than 90 per cent of Indonesia's 220 million people are Muslim, but the area around Poso is home to a roughly equal number of Muslims and Christians.
In December 1998, a drunken brawl between Muslim and Christian youths escalated into bloody clashes that left at least 1,000 people dead and forced tens of thousands more to flee.
A group of Roman Catholic men attacked an Islamic school two years later and killed up to 70 people.
A peace deal was agreed in 2002, but sectarian tensions around Poso flared again after the beheadings of the schoolgirls and religious tensions in the area remain high.