The injunction followed a July 10 ruling by Cote finding Apple conspired with five publishers to undermine e-book pricing established by the dominant retailer in the market, Amazon.com.
The five publishers, all of which have settled with regulators, include Lagardere SCA's Hachette Book Group, News Corp.'s HarperCollins Publishers LLC, Penguin Random House, CBS's Simon & Schuster and Verlagsgruppe Georg von Holtzbrinck GmbH's Macmillan.
The U.S. Justice Department, which sued Apple in April 2012, had initially sought an even broader injunction that could have touched on the company's agreements with suppliers of other types of content, such as movies, music and TV shows.
But Cote had made clear at a hearing last week that she would not go that far, saying she wanted the injunction "to rest as lightly as possible on how Apple runs its business."
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The Justice Department nonetheless welcomed the injunction.
"Consumers will continue to benefit from lower e-books prices as a result of the department's enforcement action to restore competition in this important industry," Assistant Attorney General Bill Baer said in a statement.
Apple said on Friday that it would appeal the injunction.
"Apple did not conspire to fix e-book pricing," said company spokesman Tom Neumayr. "The iBookstore gave customers more choice and injected much-needed innovation and competition into the market."