The U.S. Tennis Association announced the 2006 champion's withdrawal.
Sharapova has played only one match on tour since her second-round loss at Wimbledon in June.
"Maria Sharapova is one of the great warriors of the tennis world," USTA Executive Director and COO Gordon Smith said. "If she withdrew, there's a serious issue."
Sharapova originally was seeded third at the U.S. Open. The USTA said 2012 Wimbledon runner-up Agnieszka Radwanksa would shift from No. 4 to No. 3, and all other seeded players below her would move up a spot, too.
The USTA said Anastasia Pavlyuchenkova would become the No. 32 seed.
The draw for the year's last Grand Slam tournament is Thursday. Play begins Monday.
Sharapova's surprising exit caps a tumultuous couple of weeks for the four-time major title winner and former No. 1 player.
The Russian was sidelined by a hip injury after Wimbledon. Then she hired Jimmy Connors as her coach, an arrangement that lasted all of one match, a loss.
Sharapova last skipped the U.S. Open in 2008, when she was off the tour for about 10 months because of surgery on her right shoulder.
She won her first major title since that operation at last year's French Open, completing a career Grand Slam.
Earlier Wednesday, former top-10 player Mardy Fish of the United States withdrew from the U.S. Open, citing personal reasons.