Smoke was reported around 1:50 p.m. on the tracks in the tube that take trains from San Francisco to Oakland, BART spokesman Linton Johnson said.
An electrical issue on train tracks caused a loss of service to a substation near the entrance to the tube from the Oakland side, BART officials said.
The malfunction prompted BART officials to shut down power to one of the two sets of tracks.
The smoke spread to the other side of the tube where trains come into San Francisco from the East Bay, so the entire tube was shut down, Johnson said.
As of 2:40 p.m., trains were beginning to travel again on the side of the tube that usually brings trains into San Francisco, but there are still major delays because trains headed to the East Bay are also running on those tracks, Johnson said.
Trains between Pittsburg / Bay Point and San Francisco International Airport are the only ones operating through the tube on a single track, BART officials said.
Other westbound trains are turning around at the MacArthur station, while the remaining eastbound trains are turning around at Embarcadero station.
The only trains relatively unaffected by the problem are those that run between Richmond and Fremont, officials said.
Inspectors were still in the tube as of 5 p.m. to investigate the problem.
BART officials hope to have the problem fixed by tonight, but were unable to provide an estimate for when service through the tube would be completely restored.
"We want to make sure it's clear and safe to go through either side," Johnson said.
Despite the service setback, BART is offering additional trains to accommodate the fans leaving the Coliseum after a Raiders game.