Between 50 and 75 protesters took over an intersection in El Cajon, California, "stopping vehicles and breaking their car windows," police said in a statement.
"Protesters began throwing glass bottles at the police, and after the group refused to disperse, pepper balls were deployed," the statement said, adding that one man was "knocked off of his motorcycle" by protesters.
Police sometime fire pepper balls -- containing painful but non-lethal pepper spray -- into a crowd to discourage or incapacitate rioters.
Two unidentified men described as aged 19 and 28 were arrested, according to local police, who said there were no reported injuries.
Alfred Okwera Olango, 38, was fatally shot on Tuesday in the California town after police received an emergency call about a man behaving erratically and walking in traffic.
Thursday's protests came hours after Olango's mother, Pamela Benge, pleaded for nonviolent demonstrations.
"Please protest peacefully," she said at a press conference.
"We came here seeking safety," Benge said, adding that her family had come to the United States 25 years ago seeking refuge from war in Uganda.
In a viral video posted by a witness to the shooting, a woman who identified herself as Olango's sister said she had called police to help her brother who was mentally ill.
"You guys came and killed my brother," the woman wails in the widely viewed video.
El Cajon police said Olango had ignored repeated calls by officers to remove his hand from his pocket, and one officer used a Taser against him while another fired his weapon when Olango turned and confronted them.
The deaths of black men at the hands of police have spurred protests across America, most recently last week in the North Carolina city of Charlotte, where the fatal shooting of Keith Lamont Scott triggered days of unrest.
