Nadal has also been troubled by knee injuries in the past and preferred not to take any risks by continuing to play at the Paris Masters, where he has never won.
"It's not about London, it's about the longer term", he emphasised.
The Spaniard, who had his right knee strapped during his third-round win on Thursday, said he wanted to try and be ready to face Filip Krajinovic in the last eight but that "it wasn't possible to play".
Nearly nothing could separate the rivals in the shortest and longest points but Nadal had a slight advantage in the mid-range rallies, despite hitting a lot of unforced errors.
"The way that i am today i dont see myself playing three more matches, the knee is always bothering a little bit but sometimes its worse", he added. He didn't say whether he will be able to play at the ATP finals in London, which starts No. 12.
The second set was in balance after seven games, before Nadal, in search for his career 31st ATP Masters 1000 titles, made a crucial break in the eighth game, and converted his second match point in the ninth at 6-3. The 31-year-old battled wrist problems in 2014 that caused him to miss the U.S. Open, and he ended his season prematurely in October that year to undergo appendix surgery.
But Nadal had already done enough in the tournament to finish No. 1at the end of the year for the fourth time in his career, and first since 2013.
'Only thing I'm going to say, I'm going to do my treatment, do my best to be playing in London, but I can not talk about that now because it's a day that is tough enough for me to pull out from here'.
The Serbian will go up against John Isner of the United States in the last four after the big-serving American beat Argentina's Juan Martin del Potro 6-4, 6-7, 6-4.