The crowd was furious Tuesday with the "mild" verdict and attacked the court while chanting "kill, kill" as Bawengan was led away under heavy security, according to Fides News Agency.
Police tried to restore calm, firing warning shots and tear gas, but instead the angry mob turned to the streets and began targeting Christian sites.
Parish priest, Fr Saldanha, was violently beaten as he tried to stop attacks against the tabernacle and Eucharist at the Catholic Church of St. Peter and Paul on Sudirman Boulevard.
Another two churches, a Catholic orphanage and a health center of the Sisters of Providence were also destroyed in the rampage.
Bawengan, who has been in custody since Oct. 26, has also been accused of calling Islam a cruel religion.
"We are shocked by this event. Violence is never a good solution," the Archbishop of Semarang and secretary of the Episcopal Conference, Johannes Pujasumarta, told Fides News Agency.
He denounced the violence but also called for peace and reconciliation.
"We call on everyone, Muslims and Christians, to address issues with a sense of civility and in a spirit of fraternity," said Pujasumarta. "I invite the Catholic faithful and all Christians not to react to the violence. We want to be a sign of peace to all."
The incident has marred the celebration of Interfaith Harmony Week, an event endorsed by the U.N. to promote the peaceful co-existence of religions. The weeklong-event kicked off in Jakarta on Feb. 5.