It remained unclear Wednesday when the DACA recipients, also known as "Dreamers" could resume applying for renewals of their work permits as a result of the California ruling, which Alsup said should apply nationwide. Advocates said it would depend on the Department of Homeland Security, which runs the program.
The Trump administration has vowed to challenge Alsup's ruling.
"They can't go back and renew today," said Marielena Hincapié, executive director of the National Immigration Law Center. "We expect there to be a lot of confusion in communities about what that means."
DACA recipients and their advocates said Alsup's ruling adds new urgency to ongoing negotiations between Congress and the White House for a permanent solution for the young immigrants, who are pushing for a path to citizenship.
"We can't keep relying on lawsuits and different presidents to come in and upend our lives," said Bruna Bouhid, a spokeswoman for United We Dream who came to America at age 7 from Brazil and has a work permit through the program. "I don't want to go through this anymore. It's too hard. As a DACA recipient, it's too much back and forth. You don't know what your future looks like."
Attorney General Jeff Sessions announced the decision to terminate the program on Sept. 5 and said no renewal applications would be accepted after Oct. 5. Under the administration's plan, permits that expired after March 5 could not be renewed.
But Alsup ruled that while the lawsuit is pending, anyone who had DACA status when the program was rescinded Sept. 5 can renew it, officials said.
The judge did not rule on the merits of the case but said the plaintiffs would suffer irreparable harm if the Trump administration ended DACA before the legal dispute is resolved.
"Plaintiffs have clearly demonstrated that they are likely to suffer serious irreparable harm absent an injunction," Alsup wrote. "Before DACA, Individual Plaintiffs, brought to America as children, faced a tough set of life and career choices turning on the comparative probabilities of being deported versus remaining here. DACA gave them a more tolerable set of choices, including joining the mainstream workforce."
White House spokeswoman Sarah Huckabee Sanders called the decision "outrageous" and insisted that Congress must ultimately decide the fate of the DACA program.
"An issue of this magnitude must go through the normal legislative process," Sanders said. "President Trump is committed to the rule of law, and will work with members of both parties to reach a permanent solution that corrects the unconstitutional actions taken by the last administration."
In a tweet, Trump again took aim at the courts in the latest legal showdown over a Trump administration effort.
"It just shows everyone how broken and unfair our Court System is when the opposing side in a case (such as DACA) always runs to the 9th Circuit and almost always wins before being reversed by higher court," Trump wrote.
California Attorney General Xavier Becerra brought the lawsuit together with the attorneys general for Maine, Maryland and Minnesota, as well as the University of California, DACA recipients and others.
The plaintiffs said the Trump administration failed to follow the law in rescinding DACA and would cause irreparable harm by forcing immigrants to leave jobs, drop out of school and potentially be deported.
California is home to the largest group of DACA recipients — some 200,000 people.
The ruling is "an affirmation of the principle that no one is above the law," Becerra said in a telephone interview. "We said it from the very beginning: Donald Trump and this administration did not follow the rules in trying to abandon the DACA program."
Justice Department spokesman Devin O'Malley said the ruling doesn't change the department's position that DACA "was an unlawful circumvention of Congress. ... The Justice Department will continue to vigorously defend this position, and looks forward to vindicating its position in further litigation."
The administration's decision to terminate the program sparked an outcry from Democrats, moderate Republicans and a significant sector of the American public, and it has triggered an intense battle in the White House and Congress over possible legislation to give DACA recipients the right to stay here permanently.
Brian Murphy in Washington contributed to this report.