"Maria Sharapova is one of the great warriors of the tennis world," U.S. Tennis Association Executive Director and COO Gordon Smith said. "If she withdrew, there's a serious issue."
Sharapova, the 2006 champion at Flushing Meadows, has played only one match on tour since her second-round loss at Wimbledon in June.
"I just wanted to let you know that withdrawing from the U.S. Open has been a really tough decision to make. I have done everything I could since Wimbledon to get myself ready but it just wasn't enough time," read a message posted on Sharapova's Facebook page Wednesday night. "I have done many tests, received several opinions and it all comes down to taking the proper amount of time to heal my shoulder injury properly."
The posting added that Sharapova plans "on taking the next few weeks off, receiving proper treatment and rehabilitation."
She 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. Anastasia Pavlyuchenkova will become the tournament's new 32nd 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 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, at the Mason, Ohio, hard-court tournament.
Sharapova last missed 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. It's the latest setback in his bid to make a comeback on tour after dealing with heart issues.