Vanessa Judicpa and Maria Ydil showed up at the county clerk's office to get married.
But the judge will not allow marriages until at least Friday.
"Counties, such as San Francisco, around the state are not permitted yet to issue any licenses for marriage of gay couples until he has lifted his stay," county clerk Edwin Lee said.
Even so, people came to City Hall just to celebrate.
"I am very happy, I could not be happier, right now," Kaitlin Miller said.
Others came to protest.
"We are terribly disappointed but the ruling overturning the vote of 7 million California citizens," Catholics for the Common Good spokesperson Bill May said.
In 2004, the city of San Francisco performed thousands of ceremonies. Wednesday, the mayor who pushed gay marriage took more than a little pleasure in the victory.
"It's not the first step. We have had a hundred first steps. This is another step in a very long process, but perhaps the most compelling and historic," Mayor Gavin Newsom said.
Downstairs, the two women who came here to marry settled for a holy union blessing. Whether legal or not, they intend to hold a marriage ceremony in four days.
"We're still going to marry. In our hearts, we will be married," Judicpa said.
Looking Back At Prop 8
Future of Proposition 8 now in hands of judge
PHOTOS: Final day of Prop 8 trial
Prop 8 trial re-enacted on the web
Defense lawyers rest case at Prop 8 trial
PHOTOS: Same-sex marriage on trial in SF
Defense presents first witness in Prop 8 case
SF economist says gay marriage ban costs city
Prop 8 attorneys talk history of marriage
Groundbreaking same-sex marriage trial starts in SF
Judge refuses to dismiss Prop 8 suit
San Francisco joins federal battle over Prop 8
Governor wants speedy Prop 8 resolution
Prop 8 fight may head to U.S. Supreme Court
Couples challenge Prop 8 with lawsuit
PHOTOS: Prop 8 upheld in California
Castro District reacts to Prop 8 ruling
Calif. high court upholds gay marriage ban
Hundreds pray on eve of Prop 8 ruling
Justices hear Proposition 8 arguments
Mormon churches role in Prop 8 investigated
Court agrees to hear Prop 8 challenges
California remains conflicted about Prop 8
Prop 8 constitutionality challenged
No on 8 campaign concedes defeat
Same-sex couples scramble to get married
Proposition 8 campaigning begins