Less than an hour before his scheduled second round match against Fernando Verdasco, Nadal said his doctors had advised him to pull out of the tournament due to concerns about a pain in his abdomen.
The 32-year-old Spaniard said he did not yet know if he would be able to play in the eight man season ending championships which start in London on 11 November.
“I would love to be in London,” he added. “But the most important thing for me is to be healthy and to be healthy to compete weeks in a row.
"It’s not something that I was able to do this year. I’ve played in only nine tournaments and have retired in two. That’s the point. I have to think a little bit about the long term.
“I want to keep playing tennis for a couple of years and if I am to do that then I havbe to do the logical thing and the logical thing is not to play here in Paris. As for London, there isn’t a clear answer now.”
Nadal’s place in the second round was given to Malek Jaziri who lost in the final qualifying round on Sunday.
Djokovic has not been number one since November 2016. In fitting symmetry, he lost the slot to Andy Murray at the Paris Masters. Roger Federer and Nadal have also occupied top spot since his demise.
Djokovic’s rise to supremacy comes on the back of his triumphs at the Grand Slam tournaments at Wimbledon and the US Open. The 31-year-old has also hoisted Masters titles in Cincinnati and Shanghai.