Philip Morris, the nation's largest tobacco company, claims the ban violates its First Amendment right of free speech by putting an end to cigarette advertising and displays in the pharmacy stores.
But city lawyers wrote in their brief, "The sale of a product is conduct, not speech."
They said Philip Morris is still free to pay pharmacies to display tobacco advertisements.
Wilken will hold a hearing in Oakland on Oct. 30 on the tobacco company's request for a preliminary injunction.
Last month, she declined to grant a temporary restraining order that would have blocked the ban from going into effect on Oct. 1.
A San Francisco Superior Court judge also refused to suspend the ordinance in a separate lawsuit filed by Walgreen Co., and the measure took effect as scheduled.
Lawyers from the office of City Attorney Dennis Herrera argued in today's filing that Philip Morris' free speech claim shows "no respect for the Constitution (and) no respect for the power of cities to protect the health of their citizens."
The brief contends that if the measure "can prevent just a few young people from taking up smoking, becoming addicted to nicotine, and developing cancer, that would greatly outweigh any minimal, speculative financial loss that might be incurred by the tobacco industry."
Philip Morris argued in its Sept. 25 lawsuit that the purpose and effect of the ordinance is "to suppress communications directed to adult smokers" in violation of the company's free-speech right.