Superior Court Judge Ronald Quidachay also consolidated two lawsuits against the city into one action, paving the way for a March hearing.
Lawyers for two groups opposed to same-sex marriage had asked Quidachay to force San Francisco to stop issuing the marriage licenses.
The attorneys argued that the practice violated the terms of Proposition 22, the state initiative that in 2000 limited marriage to a union between a man and a woman.
But Quidachay said there was no reason to stop San Francisco before next month’s hearing.
“You have not shown evidence of immediate, irreparable harm,” he told attorneys.
Lawyers for the opponents on Friday promised to file a motion excluding Warren from the case, but declined to say why.
The city has asked that Warren preside, while opposition groups requested Quidachay.
As opponents vowed to press on with their case, scores of same-sex couples were married across the street in City Hall on Friday, including state Board of Equalization member Carole Migden and her partner.