The object was found near Cyril Magnin and Market streets at 7:20 a.m., police said. A bomb squad was sent to the scene to investigate.
Police asked BART not to allow trains to run through the Powell Street station during the investigation, a BART employee said.
Trains in both directions were turned around before they reached Powell Street, and riders were advised to expect major delays.
Shortly before 8 a.m., streets reopened and BART service resumed through the area. A BART employee said there were still residual delays of about 15 minutes.
San Francisco Municipal Railway service was also affected.