Citing left knee tendinitis, the third-ranked Nadal hasn't played a match since June 28, when he was upset in the second round of Wimbledon by 100th-ranked Lukas Rosol.
Nadal also pulled out of the London Olympics and a hard-court tuneup tournament in Cincinnati.
The Spaniard won the 2010 U.S. Open to complete a career Grand Slam and was the runner-up to Novak Djokovic last year.
U.S. Open tournament director David Brewer says in a statement Tuesday: "Rafa has informed us that he will not be ready to compete at the U.S. Open this year."
Play begins at Flushing Meadows on Aug. 27.