He joins world number four Ivan Ljubicic, U.S. Open runner-up Andy Roddick and Argentine David Nalbandian, who all withdrew over the past few days, citing injuries or illness.
Nadal described his injury as not serious and he should be back in action for the season-ending Masters Cup, which will feature the top eight players in the ATP race from November 12th-19th in Shanghai.
The 20-year-old Nadal, who has triumphed at the last two French Opens, has never entered the main draw at the Paris Masters, losing in qualifying in his only previous appearance as a 17-year-old in 2003.
The favourite in Paris will be Roger Federer, who underlined his brilliant form by winning the Swiss Indoors tournament in Basel on Sunday.
The world number one last visited the high-tech Bercy hall in 2003. His best results there are two quarter-final appearances that year and in the previous edition.