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.
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.
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