"Unfortunately, I had an abdominal problem in Paris last week and I also have a foreign body in the ankle joint that has to be removed through surgery", he continued.
"I want to talk about how well he played all week", Djokovic said, as per ATP's official site.
Novak Djokovic reclaimed the world No.1 ranking on Monday after a two-year absence and is assured of finishing the year there.
The Serb is back on the top of the pile for the first time in two years, at the end of a roller-coaster season for the 14-time major victor.
This way I hope to be in top conditions for next season. Djokovic has won four titles since July with two being Grand Slams - the Wimbledon and the US Open - and other two Masters Series events in Cincinnati and Shanghai.
Nadal's decision means that Novak Djokovic is guaranteed to end the year as the leader of the world rankings.
Rafael Nadal will miss November's season-ending ATP Finals in London and have surgery on an ankle injury.
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Nadal hasn't competed since he retired from his U.S. Open semifinal because of a painful right knee.
"I'm very, very happy and proud about it".
Nadal's spot in the ATP Finals will be taken by John Isner, who has been drawn in the same group a Djokovic, Alexander Zverev and Marin Cilic. "Five months ago, it was highly improbable considering my ranking and the way I played and felt on the court".
Only a semi-final defeat at the French Open prevented him from becoming just the third man to capture a calendar Grand Slam.
Djokovic's dominant run ended on Sunday when he was beaten 7-5, 6-4 by Russian Kharen Khachanov in the Paris Masters final.
Any year in which you win an 11th title at Roland Garros, Barcelona and Monte Carlo is hardly a wasted one, and yet this has been a deeply frustrating year for Nadal.
"What Novak has achieved this season has to go down as one of the great sporting comebacks", ATP Executive Chairman Chris Kerned said.