The building on Pier 29 was vacant, but there were some cars parked in the structure when the fire broke out around 1:50 p.m., said San Francisco Fire Department spokeswoman Mindy Talmadge.
No injuries were reported.
The organization putting on the yacht race issued a statement saying it did not expect the fire to have any impact on its plans for the site.
"We look forward to moving ahead with the future construction of the America's Cup Village at Pier 27/29," said the statement from America's Cup.
Pier 29 was not yet under development by America's Cup and was still under the control of the city, the Port of San Francisco and their contractor, Turner Construction Co., the statement said.
The pier was built in 1915 and has about 115,000 square feet of warehouse space. All tenants were moved out before work began last winter on the demolition of the adjacent Pier 27 for that pier's use as a cruise ship terminal, the San Francisco Chronicle reported.
"Pier 29 is pretty much an empty shed right now," Port of San Francisco spokeswoman Renee Martin told the newspaper. "We have no tenants."
As fire crews battled the blaze, large crowds of tourists and neighbors gathered to watch, including Jon Golinger, president of the Telegraph Hill Dwellers Neighborhood Association.
"People who live here are so proud to show off our waterfront," Golinger told The Associated Press. "Thousands of people go from the Ferry Building to Fishermen's Wharf and look at this pier everyday," he said.
During the height of the fire, large flames and thick black smoke were coming from the building, but by 4 p.m., fire crews had the fire contained.
The cause of the fire was under investigation.
Traffic was stopped into rush hour along The Embarcadero, which is a main route along the city's waterfront. People were being advised to avoid the area.
