Mehserle resigned from the transit agency shortly before he was supposed to be interviewed by investigators Wednesday.
Mehserle is accused of shooting 22-year-old Oscar Grant of Hayward, who was lying face-down on the station platform when he was shot and killed early New Year's Day. Mehserle was one of several officers responding to reports about groups of men fighting on a train.
Protesters gathered in the afternoon at the Fruitvale BART station where the shooting occurred. It was peaceful at first but began to turn nasty after a splinter group left that site and marched downtown.
Protesters set fire to a trash container and tried to overturn a police car, smashing the front window. Police attempted to disperse the crowd and smaller groups of protesters marched to different areas.
Some protesters threw bottles, a window of a fast-food restaurant and other downtown stores were smashed, at least three cars were set on fire and many other automobiles were damaged. Police in riot gear threw tear gas to try to break up the demonstration.
"The crowd started to become more agitated, more hostile, started throwing stuff at the police," Oakland police spokesman Jeff Thomason said. "We gave a dispersal order four to five times over a 20-minute period, then we had our officers go in and start making arrests."
Oakland Mayor Ron Dellums went to the protest scene Wednesday night to urge for calm. He and several council members then led a group toward City Hall and further addressed them.
"Even with our anger and our pain, let's still address each other with a degree of civility and calmness and not make this tragedy an excuse to engage in violence," Dellums said. "I don't want anybody hurt, I don't want anybody killed."
Grant's family has filed a $25 million wrongful death claim against BART and want prosecutors to file criminal charges against Mehserle.