The ruling by Superior Court Judge Loretta Giorgi confirmed a tentative decision she issued a day earlier and came after she heard arguments from proponents of the ban, which would have made San Francisco the first U.S. city to hold a public vote on whether to outlaw the circumcision of minors.
Michael Kinane, an attorney for the proponents, told Giorgi that circumcision was not usually performed as a medical procedure. He also said the ballot measure included an exception in cases where circumcision was needed for health reasons.
"If you bring in your son and say my custom, my religion requires circumcision of this little boy, the state hasn't said anything on the issue, so there is not a matter of pre-emption," Kinane argued.
Giorgi, while acknowledging that "there is legitimate debate on the benefits and harms of circumcision," was not swayed and ordered San Francisco's elections director to remove the measure from the ballot.
"I don't think there is any debate ... that this mater relates to issues of statewide concern," the judge said.
The ban's sponsor, anti-circumcision activist Lloyd Schofield, said afterward that he was considering an appeal.
"We will not stop until all men are protected from this damaging and harmful surgery," Schofield said.
The citizens' initiative, which qualified for the ballot in May, would have made the practice a misdemeanor punishable by a fine of up to $1,000 or up to one year in jail. The measure did not offer exemptions for religious rituals such as the Jewish bris or Muslim khitan.
The city attorney's office had joined several Jewish organizations and Muslim parents in challenging the ban in court.
"It is up to parents to make the choice whether or not to have their baby boys circumcised," said Abby Michelson Porth, associate director of the Jewish Community Relations Council. "We did not want to have Mr. Schofield legislating our religious traditions."
Backers had argued the ban was necessary to prevent circumcisions from being forced on children. Kinane pointed out Thursday that the federal government bans female circumcision.
"The U.S. government has said when you are looking at little girls we don't care if it's a matter of custom or ritual, you can't circumcise them unless there's a matter of medical necessity," he said.
Critics contended the initiative posed a threat to families' privacy and to constitutionally protected religious freedoms. They cited comic books and trading cards distributed by the measure's proponents that carried images of a blonde, blue-eyed superhero and four evil Jewish characters.
Outside the courthouse, anti-circumcision activists carried signs with slogans like "I did not consent to male genital mutilation" and a leaflet claiming that circumcision diminishes men's sexual pleasure.
San Francisco parent Jenny Benjamin, a plaintiff in the lawsuit to overturn the ban, said seeing people compare circumcision to child abuse made "my stomach churn."
"I don't know about you, but some of the decisions my parents made for me I wasn't thrilled about, but I didn't take it to voters," Benjamin said. "It seems a little extreme. It seems a lot extreme."