Jakarta resident Antonius Richmond Bawengan, 58, was found guilty of distributing books and leaflets that "spread hatred about Islam" and sentenced to the maximum five years in prison.
Islamic hard-liners shouted during the rioting that the man should have received the death penalty. Anti-riot police fired into the air to disperse the crowd.
The violence started in front of the District Court in Temanggung where the trial was held and spread to surrounding neighborhoods, police spokesman Col. Djahartono said.
Witnesses said at least nine people were rushed to the hospital with injuries and police led away some protesters for questioning.
The mob set two churches on fire and threw rocks at a third and a school building. They also torched a police truck, three cars and six motorcycles. Calm was restored about four hours later.
Indonesia's constitutional court upheld the blasphemy law last year as not limiting religious freedom and vital to religious harmony in the secular nation. Activists argued the law discriminates against believers outside the mainstream of six officially recognized faiths.
They also say the law is used largely to defend Islam, the dominant religion of Indonesia's 235 million people.