District Judge Robert Summerhays granted an injunction to Republican state attorneys challenging the halting of checks known as Title 42.
The policy, introduced by Donald Trump in 2020, was due to expire on 23 May.
The US Department of Justice said it would appeal.
Aimed at stopping virus spread in migrant holding facilities, Title 42 was twice extended by President Biden.
More than 1.7 million people have been expelled under the policy.
On Friday, Judge Summerhays in Lafayette, Louisiana, ruled that the policy would stay in place while a lawsuit by more than 20 states played out in court.
He backed the states’ argument that the Biden administration had failed to follow procedures requiring notification and time to gather public comment on the plans to end the policy.
And the judge also said that states had made the case that they would suffer harm if the restrictions ended.
The White House said it would comply with the ruling, but would also launch an appeal.
“The authority to set public health policy nationally should rest with the Centers for Disease Control (CDC), not with a single district court,” White House Press Secretary Karine Jean-Pierre said in a statement.
Mr Biden had been under pressure from his Democratic Party to end the controversial order, with critics arguing that its public health benefits failed to outweigh harm to the rights of migrants.
Title 42 allows US authorities to expel migrants seeking asylum without being given the chance to put forward their case. Children and some families are exempt.
Though Mr Biden had pledged to reverse Trump-era immigration policies while in office, the CDC under his administration extended Title 42 in August 2021, and again in January, due to the spread of the Delta and Omicron variants, respectively.
But in April, the CDC said it was ready to rescind the policy given the current, more favourable public health outlook and after consulting with the Department of Homeland Security (DHS).
However, Republicans – and some Democrats – warned that repealing Title 42 could lead to a surge in migrants at the US-Mexico border.