In Oakland, demonstrators flooded a highway, throwing rocks at police who responded with tear gas.
One person was hit with a hammer in Berkeley trying to stop another protestor vandalising a shop.
Peaceful protests continued elsewhere on Sunday, including Philadelphia and New York City.
Protesters have been angered by the deaths of Eric Garner, killed in a chokehold, and Michael Brown, who was shot dead by a police officer.
In both cases grand juries decided not to press criminal charges against the white police officers responsible.
A wave of protests across the US, mostly peaceful, followed their deaths and the decisions not to prosecute.The protests in Berkeley began peacefully on Sunday, with demonstrators marching down a main road towards neighbouring Oakland.
But some started vandalising local businesses, smashing shop windows, lobbing bottles and setting dustbins on fire.
Protesters on the highway at Oakland tried to set a patrol vehicle on fire, according to the California Highway police.
Five people were arrested in connection with the demonstrations and two officers injured.
Similar protests on Saturday ended in six arrests and a police officer suffering a minor injury.
Elsewhere on Sunday, demonstrators held a die-in outside the Philadelphia Eagles stadium, with about 200 people lying down silently, according to local media
And several protesters temporarily shut down the Verrazano-Narrows Bridge on Monday morning, which links the New York borough of Brooklyn to Staten Island, where Eric Garner died.
