The ruling was issued Wednesday in Manhattan federal court.
Apple attorney Orin Snyder told Judge Denise Cote previously that she would set a "dangerous precedent" if she concluded that Apple manipulated e-book prices as it entered the market in 2010.
The lawsuit was filed last year against Apple and major publishers. The government previously reached settlements with five publishers.
The trial had featured testimony from executives for Apple, publishers and Amazon.com.
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