Alameda County Superior Court Judge Frank Roesch said the administration must halt the furloughs for workers represented by three unions, including Service Employees International Union Local 1000, which represents 95,000 state employees.
SEIU spokesman Jim Zamora said the ruling could affect up to 50,000 employees across state government who work at so-called "special fund" agencies, or those that receive money from sources other than the state general fund.
It was not immediately clear whether the decision would apply to employees not represented by the three unions that brought the case.
Roesch ruled against Schwarzenegger's furlough orders on two fronts: He said the administration could not take the action against employees in special fund agencies. He also said Schwarzenegger had overstepped his authority by claiming the furloughs were necessary to deal with a budgetary emergency.