Earlier, police said 28 people were arrested before reducing the number Sunday morning.
The 25 arrested face charges ranging from curfew violations, rioting in the first degree, theft by unlawful taking, possession of a controlled substance and trafficking marijuana, police spokesman Dwight Mitchell said.
At least three of those arrested or cited were from out of town, Mitchell said.
Louisville Mayor Greg Fischer said the protests have been largely peaceful.
The violence began just before midnight when windows at Presentation Academy and Spalding University were smashed and several buildings were sprayed with graffiti. Small explosions were sparked when a car in the Spalding parking lot was set on fire with fireworks inside.
Police and firefighters responded to put the car fire out.
Aerial video taken from a LMPD helicopter showed a fire burning in the street near the church. Police also released videos showing shattered glass doors and a heavily damaged light sign just off the street.
The protesters who gathered inside the church were asked to remain there while police investigated and secured the area.
Police made several arrests following the car fire incident and at least 25 arrests overall Saturday night.