The court jailed Ahmadiyah member Deden Sudjana for six months, a heavier term than many of the attackers received.
Three Ahmadiyah members were bludgeoned to death in an attack by a 1,000-strong mob of hardliners in February. No-one was charged with murder.
US-based Human Rights Watch said Sudjana’s sentence was appalling.
“It seems like the Ahmadiyah face blatant discrimination not just from Islamic militant mobs, but also from an Indonesian court,” said the group’s Elaine Pearson.
Sudjana was hit with a machete and almost had his hand severed during the attack, which pitted about 20 Ahmadiyah followers against more than 1,000 fanatics in the village of Cikeusik, west Java.
But the court ruled that he had disobeyed a police order to leave the scene, and had been filmed punching another man.
Sudjana told the AFP news agency that the verdict was embarrassing.
“I’m purely a victim who has been criminalised in my own country,” he said.
“There was no police order to evacuate and I hit the man because he entered our house of worship, calling us infidels, and ordered people to kill us. Isn’t it normal that I hit the man as an act of self-defence?“
Video footage of the attack shows crowds of hardliners beating a small group of Ahmadis as police watch.
So far 12 of the attackers have been found guilty of minor offences and sentenced to between three and six months.