Protesters earlier in the day marched up San Francisco's Market Street from the waterfront to City Hall. The demonstrators briefly lay down on the street in the middle of the city's shopping district for a so-called die-in.
Police cordoned off nearby Union Square, barring entry out of concern that a plan was underfoot to topple the city's giant Christmas tree. No attempt was made on the tree or any violence reported.
Oakland police said 2,500 to 3,000 people held a largely peaceful march in the downtown area there to protest police killings of unarmed black men.
Police spokeswoman Johnna Watson said that hours later a crowd of about 500 remained and officers began making arrests.
She said at least 45 people were arrested for crimes such as vandalism, failure to disperse and resisting arrest.
By midnight Saturday there were no reports of any protest activity in Oakland.
Protesters on both sides of the San Francisco Bay carried signs that read "black lives matter" and chanted slogans and songs opposing police brutality.
Earlier in the day, police took down effigies of three black victims of lynching that were hung on the UC Berkeley campus Saturday morning.
Investigators believe the cardboard cutouts of life-sized photographs of lynching victims were connected to a smaller protest in Berkeley at noon. Police don't know the motive or who hanged the effigies and are investigating.
"These images are very upsetting," said campus spokeswoman Claire Holmes.
Organizers of the Berkeley protest said they did not know who hanged the effigies.