The city’s legislature approved an ordinance which barred the sale, manufacture or distribution of e-cigarettes on Tuesday.
The ban will come into effect when the mayor signs the legislation, which is expected to happen next month. It will create a $1,000 fine for each violation by vendors.
Supporters of the move said it would help tackle nicotine addiction among the young and noted that the health impacts of vaping remain largely unknown given it is such a new phenomenon.
However critics and e-cigarette producers warned that it would drive more people to smoke traditional cigarettes, which carry more serious health impacts.
Vaping involves drawing on e-cigarettes, which are battery-powered devices that allow users to inhale addictive nicotine liquids that are often fruit flavored.
The practice has soared in popularity among young Americans in recent years. Some 3.8 middle and high school students were found to have vaped in 2018 - an increase of 1.5 million.
London Breed, the San Francisco mayor who says she will sign the legislation, argued that the change would help protect the city’s children.
"We need to take action to protect the health of San Francisco's youth and prevent the next generation of San Franciscans from becoming addicted to these products," Ms Breed said.
She added that e-cigarette companies were "targeting our kids in their advertising and getting them hooked on addictive nicotine products".
However critics questioned whether ban the would drive users back to cigarettes. E-cigarettes do not contain the cancer-causing products found in tobacco.
An editorial in the Los Angeles Times noted that regular cigarettes were still for sale in San Francisco, arguing that "it's bad public health policy to come down harder on the lesser of two tobacco evils."
Juul, a leading market-leading e-cigarette which is based in the city, also publicly criticised the decision.
The company warned in a statement that the ban would "drive former adult smokers who successfully switched to vapor products back to deadly cigarettes, deny the opportunity to switch for current adult smokers, and create a thriving black market".
Unlike an e-cigarette ban in force in Singapore, the San Francisco legislation does not restrict the use of vaping products - only sales, manufacturing and distribution.
Recreational cannabis use has been legal for adults in California since January last year.