The company must now pay $450 million as part of a settlement, but it maintains it did nothing wrong.
US District Court Judge Denise Cote originally took issue with the settlement because Apple could end up only paying $70 million.
After the tech giant agrees to pay millions in the e-book price-fixing lawsuit, the presiding judge says, "I'm concerned about the terms of the settlement."
The settlement hinges on the success or failure of the company's appeal of a ruling that found it conspired with publishers to fix prices.
Amazon says customers who previously purchased books from the publishers involved in the Apple e-book settlement are estimated to receive between $0.73 to $3.82 per Kindle book.
The settlement comes less than a month before the scheduled beginning of the trial, in which $840 million in damages was sought from Apple.
With an impending trial in June, Apple CEO Tim Cook maintains that the company had nothing to do with facilitating a conspiracy to raise prices of e-books.
Now all that's left is Apple. The Justice Department says it will continue to litigate against the electronics giant for allegedly conspiring with Macmillan and four other big book publishers to raise e-book prices.
The European Union's executive arm says that if the solutions are deemed suitable, they will be enacted and the companies will be off the hook.
Court's approval of Department of Justice deal with three of five book publishers accused of fixing e-book prices is bad news for Apple.