U.S. District Judge Gregory Woods in Manhattan said the rule was "arbitrary and capricious" because the Department of Labor failed to justify it or account for its costs to workers, which the states estimated at more than $1 billion annually.
In a 62-page decision, Woods also said the rule conflicted with the broader worker protections under the federal Fair Labor Standards Act, adding that the Labor Department had recognized joint employer liability since 1939.
"If the Department's interpretation were 'clear' (or even permissible), some court would have probably adopted its rationale," Woods wrote. "But the Department has found not a one. Over eighty years later, this dog has yet to bark."
Narrowing the joint employer standard has long been a goal of such companies as McDonald's, Amazon.com, FedEx and hotel operators that depend heavily on franchises or outsourcing.
Led by New York and Pennsylvania, the mostly Democratic-leaning states said the administration's rule would make it harder to hold companies liable for violations by franchisees and contractors of minimum wage and overtime laws.
A spokesman for the Labor Department said it is disappointed with the decision and will review its legal options.
The attorneys general of New York and Pennsylvania had no immediate comment.
Under the revised rule, companies would be treated as joint employers of franchise and contract workers if they set their pay, and controlled hiring and firing processes, among other factors.
The rule set aside Obama administration guidance that the employment relationship hinge on "economic realities," such as the work being performed and companies' influence over the workplace environment.
Woods was appointed to the bench by former President Barack Obama.