“The changes to the industry have already happened,” said Mike Shatzkin, the founder and chief executive of the Idea Logical Company, a publishing consultant.

Since those settlements have gone into effect, prices on many newly released and best-selling e-books have gone down. One New York Times best-seller, “And the Mountains Echoed,” by Khaled Hosseini, is sold on Amazon.com for $10.99. But other e-books seem to have held closer to presettlement prices: “The Ocean at the End of the Lane,” by Neil Gaiman, is listed for $12.80 on Amazon.com.

The antitrust suit underscored the turmoil in the book industry as readers shift from ink and paper to electronic devices like tablets and smartphones, where they can buy books with the push of a button. The publishers want to embrace new media, but they are also trying to protect their profits and retain control of their businesses.

A recent survey of the publishing industry revealed that in the United States, e-books account for 20 percent of publishers’ revenue, more than $3 billion, up from 15 percent the year before. Amazon.com dominates the e-book market.

The outcome will probably inflict some damage to Apple’s reputation. The judge’s decision casts Apple as a cold and manipulative bully whose actions have harmed consumers, contrary to the way the company markets itself, as a maker of products that improve people’s lives.

Apple’s brand has already been under attack. Even though the company remains wildly successful, with iPhones and iPads flying off the shelves all over the world, its stock price is sagging and its tax practices and manufacturing processes have been under public scrutiny. Its stock fell 0.4 percent on Wednesday.

Judge Cote said e-mails and spoken statements by Mr. Jobs, the company’s charismatic leader, who died in 2011, made clear he knew publishers were unhappy with Amazon’s pricing of $9.99 for e-books, and that Apple’s entry would drive up prices across the industry.