Murhali Barda, head of the Islamic Defenders Front (FPI) in Bekasi, a city to the east of Jakarta, was convicted of "unpleasant deeds" in an attack on a priest and a Christian elder last September.
Sentencing Barda to five-and-a-half months in prison, Judge Wasdi Permana said he had "misused his authority as a cleric. He had urged protesters to disrupt the church's worship activities."
Separately, 12 others were jailed for between five and seven months over the attack, in which one of the Christians was beaten with a stick and the other was stabbed.
Two hundred radical Muslims shouted "Allahu Akbar" (God is Greater) and "Free Murhali" outside the court as 350 police officers guarded the trial.
Barda rejected the court's finding and vowed to appeal."I should have been freed. The accusations were all wrong," he said after the trial.
Barda has previously said he had taken part in protests against Christian church services as a Bekasi resident, not as a member of FPI, which is known to have carried out armed attacks on moderates and minorities.
The FPI does not formally advocate mass attacks, but does share the jihadists' agenda of implementing sharia law in Indonesia.
Some members have been arrested in connection with terror plots but the group has always maintained they were acting on their own.
Religious violence has been on the rise in Indonesia in recent months, mainly by Muslims, who make up around 80 percent of the country's 240 million people, against minority groups.
An Islamist mob beat and stoned to death three members of a Muslim minority sect in West Java this month.
Two days later another mob of enraged Muslims rampaged through the streets of Temanggung, Central Java, and set fire to churches after a Christian man was jailed for insulting Islam.