Investigators said someone threw multiple explosive devices, causing minor injuries to several officers. They are expected to make full recoveries.
Naperville's police chief said the people behind the violence Monday came in from out of town.
The FBI is investigating the incident, police said.
RELATED: Downtown Naperville looting leaves businesses damaged
Earlier on Monday, a large crowd gathered in Naperville for a peaceful protest in which the police chief knelt in solidarity with demonstrators.
But just after 10 p.m., large crowds were reported near Aurora and Main Street. According to witnesses, outside groups pulled up and damaged multiple businesses in downtown. One witness said a restaurant and a jewelry store had its windows smashed.
During ABC7's 10 p.m. newscast, the crew on the scene reported hearing a group say "let's start looting" before trying to kick open the doors at a Walgreens just off Main Street.
A SWAT Team was called to the Walgreens after a group of people threw rocks and caused damage to the building, police said.