Passed last November and due to come into effect in June, the law is facing belated but fierce opposition from myriad small businesses. More strikingly, it has come under attack from an unlikely coalition of United Airlines and the Roman Catholic Church.
Originally viewed as an unsurprising gesture by a city that is famous for its liberal attitudes towards the gay lifestyle, the law is now taking centre-stage in national debate about homosexual rights, alongside the steps being taken by Hawaii to becoming the first US state to legalise gay marriage.
The city recently revealed that it was holding off giving final authorisation to United, the country's second-largest airline, to build huge new kitchen and equipment-repair facilities at San Francisco airport until the company gives an assurance that it will comply with the ordinance. United is baulking and has threatened to move the facilities - and 7,000 jobs - to Oakland, on the other side of San Francisco Bay.
This week, meanwhile, has witnessed a verbal flare-up between the city's mayor, Willie Brown - the ordinance's principal defender - and San Francisco's Catholic archbishop, William Levada. The spat has led one gay and lesbian group to ask the Pope to remove Archbishop Levada.
The ordinance would oblige all companies, government agencies and charities that have contracts with the city to give benefits such as health insurance and pension rights to partners of employees even if they are not married. Several locally-based companies, such as Levi Strauss and Apple Computer, have had such policies for years.
The religious clash centres on the work of Catholic Charities, an affiliate of the Catholic church in the city that offers shelter and food to the homeless and to Aids victims. It draws part of its budget from city coffers. Mr Brown says the charity must adhere by the new law, but Archbishop Levada argues that to do so would violate Catholic teachings and doctrine. He is threatening to sue the city if it does not relent.
Mayor Brown has shown little sign of backing down. Indeed, his office seems prepared to contemplate simply ending the city's relationship with Catholic Charities and turning to alternative groups. Nor does there seem to be sympathy for many small businesses facing the almost impossible task of finding insurance companies willing to cover non-married partners.
As for United, it had already begun building the new facilities when the city adopted its position. Moreover, the airline is being asked to extend the new benefits not only to 20,000 employees based in the San Francisco area, but to its entire US workforce of 86,000.