The nine-time French Open champion and 14-time Grand Slam title winner confirmed he will have his appendix removed on November 3.
Given the circumstances the 28-year-old Spaniard said there was no logic in him competing at either next week's Paris Masters or the eight-man World Tour Finals in London from November 9.
"This is the day to say goodbye for the season," said Nadal.
"It's the day to say I had a good first six months this year. But it was hard after that with back and (three-month summer) wrist problems and now the appendix. I'm not going to play Paris or London, I'm not competitive enough to do that.
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Top seed Roger Federer turned in another command performance, mowing down fifth-seeded Bulgarian Grigor Dimitrov as the Swiss continued his bid for a sixth home trophy.
Federer posted a 7-6 (7/4), 6-2 win to set up a semi-final with the biggest server in the game, Ivo Karlovic after the eighth seed beat German Benjamin Becker 6-4, 6-4.
"It's like a penalty shootout playing him," said Federer of the leading ace-maker on the ATP this season with more than 1,000.
Federer's win was his 65th of the season and lifted his record at the tournament to 54-9.
Nadal, who had been taking antibiotics to treat appendicitis since the Chinese swing of the tour earlier this month, said his goal is to have a month of training in December when his physical problems are mended.
"If I play the last two tournaments, I would not be competitive and would have no chance to win. It is better for me to recover. I hope to be back at the start of 2015 ready for anything.