US District Judge Allison Burroughs' order provides temporary relief to the thousands of international students who were faced with being forced to transfer under a policy that the Ivy League school called part of the administration's broader effort to retaliate against it for refusing to "surrender its academic independence".
The administration may appeal Burroughs' ruling.
In a lawsuit filed in Boston federal court earlier on Friday, Harvard called the revocation a "blatant violation" of the US constitution and other federal laws, and had an "immediate and devastating effect" on the university and more than 7000 visa holders.
"With the stroke of a pen, the government has sought to erase a quarter of Harvard's student body, international students who contribute significantly to the University and its mission," Harvard said.
"Without its international students, Harvard is not Harvard," the 389-year-old school added.
Harvard asked a federal judge to block the revocation, citing "the immediate and irreparable harm inflicted by this lawless action".
The case was assigned to US District Judge Allison Burroughs.
White House spokeswoman Abigail Jackson dismissed the lawsuit.
"If only Harvard cared this much about ending the scourge of anti-American, anti-Semitic, pro-terrorist agitators on their campus they wouldn't be in this situation to begin with," Jackson said.
"Harvard should spend their time and resources on creating a safe campus environment instead of filing frivolous lawsuits," she added.
The termination of Harvard's Student and Exchange Visitor Program certification, effective with the 2025-2026 academic year, was announced by Homeland Security Secretary Kristi Noem and affects about one quarter of Harvard's students.
She said terminating the certification was justified because of Harvard's "fostering violence, anti-Semitism and co-ordinating with the Chinese Communist Party".
In a letter to the Harvard community, the school's president Alan Garber condemned the administration's actions.
"The revocation continues a series of government actions to retaliate against Harvard for our refusal to surrender our academic independence and to submit to the federal government's illegal assertion of control over our curriculum, our faculty, and our student body," Garber wrote.
Harvard enrolled nearly 6800 international students in its current school year, equal to 27 per cent of total enrolment.
In its complaint, Harvard said the revocation would force it to retract admissions for thousands of people and has thrown "countless" academic programs, clinics, courses and research laboratories into disarray, just a few days before graduation.
The revocation follows Noem's demand on April 16 for a large trove of information from Harvard about student visa holders.
In a letter to Harvard, which was attached to the complaint, Noem said the information was needed because the university had "created a hostile learning environment for Jewish students due to Harvard's failure to condemn anti-Semitism."
On Thursday, Noem said Harvard could restore its certification by turning over within 72 hours a raft of records about international students, including video or audio of their protest activity in the past five years.
In his letter on Friday, Garber said Harvard responded to Homeland Security Department requests as required by law.
