Police received a report of a suspicious device in the 100 block of Terry Francois Street at 8:46 a.m., police spokesman Officer Albie Esparza said.
The department's bomb squad responded and police shut down Third and China Basin streets, Esparza said.
San Francisco Municipal Railway service on the KT-Ingleside/Third Street line was disrupted by the incident, and bus shuttles were set up for the affected riders, Muni spokesman Paul Rose said.
The streets were reopened and service resumed at 11:58 a.m., Rose said.
No injuries were reported.