Nadal was advised by his doctor to withdraw from the September 26 - October 4 tournament to recover from a stomach muscle problem that bothered him in the US Open earlier this month, Suwat Liptapanlop, president of the Lawn Tennis Association of Thailand, told a news conference.
Nadal lost his US Open semifinal in straight sets to Argentina's Juan Martin del Potro, who went on to capture his first Grand Slam title with a victory over top-ranked Roger Federer in the final.
Nadal canceled a pre-tournament vacation scheduled to start on Wednesday on the Thai island of Krabi, Suwat said.
The injury also forced Nadal to sit out Spain's Davis Cup semi-final win over Israel on the weekend.
Nadal has struggled with injuries this season, with sore knees keeping him off tour for all of June and July, forcing him to skip a title defense at Wimbledon, and the abdominal muscle issue flaring up during his third-round victory over Nicolas Almagro at the US Open.