Five other Christians received eight-year terms for burying the pair, who were set upon by a mob as they drove though a Christian neighborhood on Sulawesi island a day after the Sept. 22, 2006, executions of Fabianus Tibo and two other Christian militants.
The three executed Christians had been found guilty of leading a militia that killed at least 70 Muslims during a 1999-2002 religious war on the island that led to the deaths of at least 1,000 people from both faiths.
The South Jakarta District Court found all 17 men guilty Thursday of violating anti-terrorism laws.
"It has been proven that they carried out acts of terror together and tried to hide the crime by hiding the bodies," said head judge Ahmad Subari.
Two of the 12 found guilty of murder were sentenced to 14 years in jail each, while the other 10 got 12 years.
It was not clear whether any of defendants intended to appeal.
The executions of the three Christian militiamen took place despite an appeal by Pope Benedict XVI to spare the men and claims by human rights groups that their trials were unfair. The revenge killings were the bloodiest incident in several days of protests at the executions.
More than 90 percent of Indonesia's 220 million people are Muslims, but Sulawesi has a roughly equal number of Muslims and Christians. Earlier this year, police rounded up several Islamic militants accused in bombings and shootings since 2002, and the island has been peaceful since then.