SEIU Local 1021 spokesman Des Patten said talks with BART management "didn't make much in the way of progress" after ending around 7 p.m. and that bargaining will be held off for a few days.
He said the two sides will resume talks toward the end of the week.
"We're taking a couple of days off," Patten said. "We've been working continuously everyday."
Management issued a statement following Sunday's negotiations.
ART officials said the "latest attempt to reach a fair contract went unanswered tonight as the unions walked out of negotiations without responding to the current (management) proposal, despite the fact BART increased its wages and benefits offer" since last week.
Patten said the unions are hopeful that the labor dispute will be resolved before the end of the governor's requested cooling off period.
Gov. Jerry Brown on Friday filed a petition requesting the court order, which prevents a strike and also prevents the transit district from locking out its workers any time before midnight on Oct. 10.
Sunday morning, San Francisco Superior Court Judge Curtis Karnow ordered the cooling off period at a special hearing after finding that a strike would significantly disrupt public transportation services and endanger the public.
Contract negotiations resumed Sunday afternoon at Caltrans headquarters in Oakland around 1 p.m., BART spokesman Rick Rice said.
The two unions representing BART workers, the Service Employees International Union Local 1021 and the Amalgamated Transit Union Local 1555, had threatened to strike again over issues including wages and health care and pension contributions.
The SEIU represents 1,430 BART mechanics, custodians and clerical workers and the ATU represents 945 station managers.
BART trains have been running since a four-day strike ended on July 5.
If no agreement is reached before the end of the 60-day cooling off period, workers will then have the right to strike at any time.