Take any San Francisco bound train and get off at the Civic Center station. Take the BART escalator up two levels to the top, exit the BART turnstile, then find a nearby MUNI turnstile, pay your $1, and take the MUNI escalator down one level. (You never leave the station.) From here on follow the MUNI directions.
For more information on BART in general, see the Bay Area Rapid Transit home page.