The new law allows transgender students to take part in school programs, such as sports, and use bathrooms based on their gender identity rather than their sex.
About 5,000 petition signatures taken in Mono and Tulare counties were submitted after a 90-day deadline expired.
Sacramento County Superior Court Judge Allen Sumner ruled they must be used because the deadline was on a Sunday and the following day was Veteran's Day.
Secretary of State Debra Bowen's chief of staff, Evan Goldberg, said Bown would comply with Sumner's order and allow it to become final without requesting a hearing.
"The secretary of state believes that the 90th day meant the 90th day," Goldberg said. "The judge in this case has ruled otherwise. And the secretary will indeed count those signatures once they are submitted by the two counties in question."
The petition group Privacy for All needs 504,000 signatures to get a repeal on the ballot. It submitted more than 619,000.
Right now counties are checking random samples to help determine how many are valid.