San Francisco police Sgt. Monica Macdonald said one protester threw a bottle at a police car. The broken glass cut the officer's face and he was transported to the hospital, where he received stiches.
Another officer was injured by a brick thrown at his chest and Macdonald said protesters threw bottles at officers as well.
BART temporarily shut down the 16th Street and 24th Street stations in the Mission District because of the unrest above the subway, BART officials said.
The demonstration began at 6:30 p.m. near the Embarcadero station, Macdonald said. Protesters marched to Union Square, where they intended to join another protest staged outside of Macy's annual tree-lighting ceremony.
Police prevented the crowd from reaching Union Square and herded the group down Market Street, where the windows of several businesses were smashed.
The protest lasted until roughly 10 p.m., and officers didn't start making arrests until approximately 9:30 p.m., Macdonald said.
Muni service was also rerouted around the demonstration, which proceeded down Market Street before moving towards the Mission.
Protesters could be heard yelling, "Missouri, Palestine, justice now," and "No justice, no peace."
Some set off fireworks and chanted, "SFPD, how do you spell murder?" as drivers in cars honked their horns in support.
The demonstrators were protesting a grand jury's decision to not indict Ferguson, Mo., Officer Darren Wilson in the shooting death of 18-year-old Michael Brown, who was unarmed.
The protests tonight were the second in the Bay Area today and followed a demonstration at the West Oakland BART station earlier in the afternoon, when activists locked themselves to two BART trains and halted service for several hours.
There have been protests every night in Oakland, except Thanksgiving night, and several in San Francisco throughout the week.
Macdonald said arrests are still in progress and the department might not have final numbers until Monday.