Clerk Ernest Dronenburg had asked the court to stop gays from marrying on grounds that Proposition 8 remains state law, the Los Angeles Times reported Wednesday.
A court spokesman said the justices voted 6-0 with Justice Kathryn Mickle Werdegar not present to deny Dronenburg's request for a temporary hold.
Lawyers for Dronenburg told the court the clerk was in "a quandary" because state officials have ordered him to give licenses to gay couples but the California Constitution continues to define marriage as between two people of opposite sex.
Sponsors of Proposition 8, the 2008 ballot measure that banned gay marriage, filed a similar request that was rejected by the court last week.
Gay rights groups like Marriage Equality USA cheered Tuesday's decision, CNN reported.