The new rule comes into effect on August 20, the San Francisco Chronicle reported, and is part of a five-year plan to lower landfill waste, net carbon emissions and net energy use to zero.
"We're the first airport that we're aware of to implement this change," airport spokesman Doug Yakel told the newspaper.
"We're on the leading edge for the industry, and we want to push the boundaries of sustainability initiatives," he said.
The ban will apply to all restaurants, cafes and vending machines, though not to planes using the airport.
It exempts brands of flavored water.
Filtered water is provided for free at 100 "hydration stations," where flyers can top up glass or metal bottles.
The airport describes itself as an "industry leader" in sustainability, installing solar panels and instructing all tenants to use fully compostable food ware including straws and utensils.
Airports in Dubai and India have announced similar plastic bottle bans, but have yet to fully implement them.
The city of San Francisco banned the sale of plastic water bottles on city-owned property back in 2014, but allowed delays and granted certain exemptions.
Global plastic production has grown rapidly, and is currently at more than 400 million tons per year.
Single-use items represent about 70 percent of the plastic waste littering the marine environment.
Each year, a million birds and more than 100,000 marine mammals worldwide are injured or killed by becoming entangled in plastic or ingesting it through the food chain.
Canada and the European Union have pledged to ban single-use plastics starting in 2021.