Oakland police pulled over a car at 11:43 a.m. on city streets near the BART station, BART spokesman Jim Allison said.
One suspect was arrested but a second ran into the BART station and onto the tracks, Allison said.
BART shut off power to the tracks and no trains were being allowed through the station. Police emptied a train at the station and searched it and the tracks.
At 12:15 p.m., BART determined that the station was safe and trains began moving through again.
Allison advised riders to expect residual delays of up to 20 minutes as trains get back on schedule.