The train, bound for San Francisco International Airport, became disabled in the tube around 8:25 a.m., BART spokeswoman Luna Salaver said.
When the train stalled, power went out in the front car, leaving some riders in the dark, Salaver said.
The incident caused lengthy delays systemwide.
Salaver said the operator went to the back of the train and used the rear-car control room to move the train back to West Oakland in manual mode. The passengers were let off and took a different train into San Francisco, she said.
The tunnel was cleared shortly before 9 a.m. but residual delays lingered. As of 10:45 a.m. service was nearly back to normal but some trains were a few minutes late.
Many BART riders posted about the experience on social media.
One Twitter user said, "Being stuck in a BART train in the transbay tube for 30 minutes this morning was pretty close to my worst commute ever."
Another rider tweeted, "On a BART train stuck in the TransBay tube, lights out, no power. This...this means that the first Kaiju attack is happening, right?"
David Brown, 25, who works at the San Francisco Massage Supply Company on 10th Street in San Francisco, opened the shop late because his train that he caught at the Ashby Station in Berkeley was stopped at West Oakland behind the stalled train for more than 30 minutes.
He said his fellow riders took the delay in stride and that the operator kept passengers informed on what was happening every few minutes.
"Nobody was huffing and puffing," he said. "People were keeping to themselves."