"The situation has been resolved. All clear, all clear," the building's occupants were told over a loudspeaker at 2:20 p.m.
The package was discovered on a conveyor belt in the building's basement mailroom at about noon, San Francisco Police Officer Albie Esparza said.
Esparza said the department's bomb squad aided in the probe.
During the two-hour investigation, occupants of the fourth through 20th floors of the building were instructed to shelter in place.
People on the first through third floors were told to move to the Turk Street side of the building, and those on the basement and sub-basement floors were evacuated.