The three Christians were executed by an Indonesian police firing squad early on Friday amid tight security in Palu, the capital of Central Sulawesi province.
Fabianus Tibo, Marianus Riwu and Dominggus Silva had been sentenced to death in 2001, after being found guilty of leading a mob in an attack that killed more than 200 people at an Islamic boarding school during clashes in the province between Muslims and Christians.
The mens' priest, Jimmy Tumbelaka, said they had been officially declared dead at 3am, although police officials said the execution was hours earlier.
The bodies of Tibo and Riwu were flown to their home town while Silva was buried in Palu.
The trio had originally been scheduled to die in August, but the executions were postponed after demonstrations by thousands of Indonesians and an appeal from Pope Benedict.
Violence has since erupted in Silva's hometown of Atambua in West Timor when thousands of Christians protested.
Elli Mali, a Red Cross official, said the demonstrators broke into a jail and freed about 200 prisoners.
"The mob numbers in thousands. I ran into some of the prisoners and they said, 'I'm free!'" Mali told Reuters.
"We are deeply disappointed that despite the debate on the death penalty that the case had sparked across Indonesia, the state went ahead and killed these three men"
The protesters threw stones and burned the local prosecutors' house, Indonesian media and police said.
Julito Borges, a policeman in Atambua, told Reuters that two policemen were injured but the crowd had begun to disperse.
In Palu, Bishop Joseph Suwatan, whose diocese oversees North and Central Sulawesi, urged the people in Palu to remain calm.
Jusuf Kalla, the Indonesian vice president, appealed for calm following Friday's sectarian violence, which left at least five people injured. He said the overnight executions had nothing to do with religion.
But the European Union condemned the executions, urging the government to ban the death penalty and repeating calls for a dialogue between religions.
Friday's violence took place on Sulawesi and the nearby islands of Flores and Timor, which are dominated by Christians.
On the island of Flores, the condemned men's birthplace in East Nusatenggara province, machete-wielding youths terrorised residents and tore apart the local parliament, breaking windows and smashing in doors and overturning benches.
On West Timor, more than 200 inmates escaped after mobs assaulted a jail in the town of Atambua, sending guards fleeing to the nearby jungle. Only 20 prisoners had been recaptured.
History of violence
But in the Poso area of Central Sulawesi, where many Christian-Muslim clashes have occurred in recent years, including the incident for which the men were prosecuted, hundreds of protesters rallied against the executions and burned tyres.
About 4,000 police and soldiers had been deployed in Central Sulawesi "to anticipate any untoward incidents", police spokesman Kilat had said earlier this week.
Human rights groups had urged Indonesia not to proceed with the executions.
Isabelle Carton, a South East Asia researcher at Amnesty International, said on Friday: "We are deeply disappointed that despite the debate on the death penalty that the case had sparked across Indonesia, the state went ahead and killed these three men."
Muslim-Christian clashes rocked Central Sulawesi from late 1998 to 2001, killing an estimated 2,000 before a peace accord took effect. There has been sporadic violence since.