The order was issued on Friday by federal Judge Denise Cote.
She is ordering Apple to make changes to its contracts to ensure it does not repeat the kind of price fixing that resulted when it colluded with publishers in 2010.
The judge ruled in July that the collusion occurred despite Apple's insistence that it acted fairly. The Justice Department said on Friday it was pleased with the order. It said consumers will benefit from lower e-book prices.
Apple spokesman Tom Neumayr says the company will appeal the July decision. He says Apple did not conspire to fix e-book pricing.