Mayor Ed Lee said in a statement that he joins riders throughout the city in their frustration at the drivers who have "irresponsibly abandoned their jobs and intentionally disrupted" service.
"This cannot continue," Lee said. "I say to our drivers, 'People count on you to do your job so they can get to theirs.'"
Most trains and buses running were at capacity.
The contract that Muni workers rejected would have given them a raise of more than 11 percent over two years. However, it also would have required them to cover a 7.5 percent pension payment currently paid by the transit agency, said Rose, the agency spokesman.
The contract would have increased operator pay to $32 an hour, making them the second-highest-paid transit workers in the country, Rose said.
Williams, the union president, called the proposal unfair and said the city had proposed unreasonable takeaways in wages and benefits.
"Our members are hard-working and all we want is fairness," Williams said.