The Justice Department said this conspiracy was designed to undercut online retailer Amazon.com's dominance of the fast-growing e-books market.
Only Apple went to trial, while the publishers—Lagardere SCA's Hachette Book Group and Macmillan, News Corp.'s HarperCollins Publishers, Pearson's Penguin Group (USA), and CBS's Simon & Schuster—settled with the U.S. government and the states.
Cote said the conspiracy resulted in prices for some e-books rising to $12.99 or $14.99, when Amazon had sold for $9.99.
"The plaintiffs have shown that the publisher defendants conspired with each other to eliminate retail price competition in order to raise e-book prices, and that Apple played a central role in facilitating and executing that conspiracy," Cote said.
"Without Apple's orchestration of this conspiracy, it would not have succeeded as it did in the spring of 2010," she added.
In a statement to CNBC later, Apple said it will appeal the ruling. "Apple did not conspire to fix ebook pricing and we will continue to fight against these false accusations," it said. "When we introduced the iBookstore in 2010, we gave customers more choice, injecting much needed innovation and competition into the market, breaking Amazon's monopolistic grip on the publishing industry."
(Read More: Battle of the App Stores: Apple, Amazon End Trademark Suit)
Cote issued her 159-page decision after a non-jury trial that ended on June 20.
The case is U.S. v. Apple Inc et al, U.S. District Court, Southern District of New York, No. 12-02826.