"The parties will continue to negotiate just as hard as they are now," California Labor Secretary Marty Morgenstern said late Thursday. "The battle's not over. The job's not done."
Thirty-five trains were put back in service in time for an expected light evening commute, the Bay Area Rapid Transit agency said.
Morgenstern said he and two top state mediators urged the bargaining parties to agree to an extension of the current labor deal. Both groups had said they were far apart in negotiations, but details were not provided.
BART workers walked off the job on Monday after negotiations broke off. The four-day strike crippled commutes across the Bay Area.
Talks resumed on Tuesday as political pressure and public pleas mounted to reach a settlement.
Key issues in the labor dispute involved salaries, pensions, health care and safety.
BART serves more than 400,000 commuters each weekday. The transit system carries passengers from the farthest reaches of San Francisco's densely populated eastern suburbs to San Francisco International Airport across the bay.
BART's last strike lasted six days in 1997.
The Associated Press contributed to this report.