Bay Area Rapid Transit trains resumed service at about 50 percent of capacity around 7:15 a.m., a little more than three hours after train service normally resumes. BART spokesman Jim Allison said 53 trains were back in service shortly after 8 a.m., about nine short of full capacity.
The system has been shut down two other times in recent months as a result of an ongoing labor dispute. BART is the nation's fifth largest commuter rail system and has an average weekday ridership of 400,000.
"If there's any consolation, this occurred on a Friday which is usually one of our lighter days," Allison said. "Had this been on a Tuesday or Wednesday, then it could've affected more people. We're sorry it happened."
Friday's computer problem began after midnight, and affected 19 trains with 500 to 1,000 passengers. Allison said computer systems were not communicating properly with track switches that route trains.
Officials had hoped to resume service at 5 a.m., but were unable to meet that deadline.
Commuters have endured two other recent BART service disruptions when workers walked off the job in July and again in October.
The shutdowns snarled the Bay Area commute, as people turned to crowded buses, ferries and roadways as alternatives.
Jill Ann Cosentino, 35, of Oakland, was at the West Oakland BART station on Friday morning, glad to be able to get to her job as an event planner in San Francisco. But she noted BART's recent problems.
"BART has been so inconsistent this year, a bad year for them," she said.
And more trouble could be brewing for the transit agency after BART's board on Thursday approved a labor agreement that ended the last strike, but removed a sick leave provision that was supported by unions.
The transit agency said the provision could cost $44 million over four years if one-third of union workers take six-week leaves each year.
BART officials announced last week that the provision had been inadvertently included in the proposed contract.
The decision created uncertainty about the fate of the tentative contract. Union representatives called the move an unfair labor practice and said they intended to discuss the matter with attorneys.