Judge Ronald Evans Quidachay denied the Campaign for California Families' request for a temporary restraining order, but he said the group had the right to a hearing on their argument that the city is violating state law.
The conservative group argued that the weddings harmed all the Californians who voted in 2000 for Proposition 22, which defined marriage as between a man and a woman.
The judge suggested that the rights of the gay and lesbian couples appeared to be more substantial.
"If the court has to weigh rights here, on the one hand you are talking about voting rights, and on the other you are talking about equal rights," Quidachay said.
Mathew Staver, a lawyer representing the Campaign for California Families, said he believes the court will ultimately decide that Mayor Gavin Newsom acted illegally when he started the process last week.
"He can't decide to grant same-sex marriage licenses any more than he can declare war against a foreign country," Staver said.
But chief deputy city attorney Therese Stewart said the failure of conservative opponents to win emergency injunctions demonstrates that the city has a strong case.
"Both judges really recognized there is nobody who is hurt by allowing gay people to marry," Stewart said.
Newsom remained defiant before the ruling, officiating at the wedding of one of California's most prominent lesbian politicians inside his offices at City Hall.
About 25 anti-gay-marriage protesters later blocked the door of the county clerk's office, lying down in front of the line and singing religious songs.
Gays and lesbians responded by belting out "The Star-Spangled Banner" until sheriff's deputies escorted the protesters out. No arrests were made.
Gov. Arnold Schwarzenegger has said the state will reject the city's same-sex marriage certificates.
In New Mexico, meanwhile, the Sandoval County clerk issued marriage licenses yesterday to 26 gay couples, some of whom then exchanged vows outside the courthouse, as more same-sex couples lined up for a chance to tie the knot.
But the office later said the licenses were invalid, after the state's attorney general issued an opinion.