BART canceled all passenger service when the strike began Friday, the San Francisco Chronicle reported.
Paul Oversier, an assistant general manager, said the train that struck the two men near Walnut Creek was hauling cars being taken to a yard for graffiti removal.
The train was being operated by an experienced engineer, Oversier said. But he said it was under computer control when it struck the two track workers.
Leaders of the union representing train operators said there would be no picketing Sunday as a gesture of respect.
The National Transportation Safety Board. is investigating the crash.
The strike began at 12:01 a.m. PDT Friday after the president of their Service Employees International Union Local 1021 walked out of contract negotiations Thursday afternoon.
Commuters were left to figure out alternative ways to get to work Friday and ended up on crowded buses and ferries and stuck in traffic, the San Jose (Calif.) Mercury News reported.
Walnut Creek resident Edward Benney, who has been commuting to San Francisco for about 19 years, said he waited in line for a bus for 30 minutes.
"The real mayhem is going to come Monday," he said. "A lot of people can take today off. They probably aren't going to work. Monday is going to be much, much worse."