The protesters had set up a camp on Market Street following a raid last week on their encampment in the city's Justin Herman Plaza, the San Francisco Chronicle reported.
Police said the group had been advised for the previous 24 hours they were on the site illegally and would be subject to arrest.
Authorities said there were no injuries reported during the confrontation as police officers moved into the camp about 4 a.m.
Protesters said they would regroup and promised to return to the site, the Chronicle reported.
Notable deaths of 2014 [PHOTOS]