Schwarzenegger wrote to Attorney General Bill Lockyer telling him to take legal action to stop the city from granting marriage licences to gay couples, saying the practice presented "an imminent risk to civil order".
The call came hours after a judge, for the second time this week, denied an urgent petition by conservative groups to halt the city's same-sex marriages, which are becoming a political flashpoint in the United States.
"The City and County of San Francisco's unfortunate choice to disregard state law and grant marriage certificates to gay couples directly undermines this fundamental guarantee," Schwarzenegger wrote.
"Because the City and County of San Francisco's actions are directly contrary to state law and present an imminent risk to civil order, I hereby direct you to take immediate steps to obtain a definitive judicial resolution of this controversy."
The governor's order for unspecified legal action by the attorney general came after 3277 same-sex couples were married by the city in its nine-day challenge to state laws barring gay marriage.
Superior Judge Ronald Quidachay was the second judge in a week to rule that the marriages could continue, for the meantime at least, saying that conservative groups had failed to prove irreparable harm was being done.
"You have not made a showing of irreparable harm. You are strong in argument but not in evidence to support the prong of irreparable harm."
"You have not made a showing of irreparable harm," he told the Campaign for California Families (CCF) that sought an injunction to block the wedding blitz.
"You are strong in argument but not in evidence to support the prong of irreparable harm," he told a packed courtroom across the road from San Francisco City Hall where scores of gay couples were wed on Friday.
The CCF had contended the city's sanctioning of gay marriage flouted the rights of voters and taxpayers who approved a popular initiative in 2000 defining marriage as the union of a man and a woman.
Quidachay also combined the politically-explosive case with a separate suit filed by another conservative group, the Alliance Defence Fund (ADF), to which he refused to grant an injunction halting the marriages on Tuesday.
"This means that there will be even more happy same-sex couples," said John Davidson of gay lobby group Lambda Legal.
"People are seeing that gays are getting married and that no one had been hurt by it and civilisation is not crumbling."
But conservative groups and a small knot of anti gay marriage protesters outside the nearby city hall, where the wave of gay marriages was underway, were furious over the refusal to stop the challenge to state law.
"This is turning upside down marriage and the vote of the people," said Randy Thomasson of the CCF.
"Citizens and children everywhere are being told the law doesn't matter.
"There are laws I don't like but I obey them, that is what makes America better than a dictatorship," he said, adding that the city's youthful new mayor was "running San Francisco like a dictatorship".