The US Department of Justice has won its antitrust case against Apple, with District Judge Denise Cote today ruling that "Apple conspired to restrain trade" by leading a conspiracy to raise e-book prices above the low prices charged by Amazon.

"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 wrote in her decision. "Without Apple’s orchestration of this conspiracy, it would not have succeeded as it did in the Spring of 2010."

Just how Apple will be punished is yet to be determined. The plaintiffs "are entitled to injunctive relief," Cote wrote. "A trial on damages will follow."

In response, an Apple spokesman told Reuters that "Apple did not conspire to fix e-book pricing. 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. We've done nothing wrong." Apple plans to appeal.

The decision from the US District Court of Southern New York is not a surprise. Cote said even before the civil trial that the government's evidence was likely strong enough to show that Apple facilitated a conspiracy.

Book publishers Penguin, HarperCollins, Hachette, Simon & Schuster, and Macmillan were named as defendants in the case as well, but all of them settled with the government in advance of trial, providing $164 million in reimbursements to consumers overcharged for e-books. More reimbursements may follow because of today's decision.

"Because Apple was found liable for violating US antitrust laws, a hearing will now take place in a separate lawsuit brought by state attorneys general, who are seeking to recover damages on behalf of consumers who paid higher prices for e-books," the Wall Street Journal reported.

Apple and the publishers were accused of fixing the standard prices of e-books at $12.99 and $14.99, above Amazon's typical rate of $9.99. Apple called the case "bizarre," saying the government is "trying to reverse engineer a conspiracy from market effect.”

UPDATE: We have broken out a detailed summary of Cote's decision into a separate article.