Nadal, who has not competed since retiring with a knee injury against Juan Martin del Potro in the US Open semi-finals on 7 September, had been due to play his Spanish compatriot Fernando Verdasco in the Paris second round.
Calling a halt in play, Djokovic went over to the struggling fan while gesturing to the umpire, as Sousa also held up his racket in a signal to stop. I really don't want that.
Since then, he has returned to full form and has won Wimbledon, Cincinnati, the US Open and the Shanghai Masters.
Roger Federer, who won his 99th career title at the Swiss Indoors last Sunday, advanced to a third-round meeting with Fabio Fognini after big-serving Milos Raonic retired before their match with a right elbow injury.More news: Open to new deal with Iran
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Despite a 15-2 head-to-head record, Djokovic lost to Cilic in the same stage in 2016 to cede his top position.
Nishikori has been in fine form ever since his comeback from an injury earlier this year.
Once he had earned an inevitable break for 2-1, consoled the Bosnian, who told him at the net that he was in no shape to continue. But Dzumhur pulled out with a back problem before the match could be completed, trailing 6-1, 2-1 at the time. "I'm happy to play well today".
There may be an element of the precautionary with his, as the ATP Tour Finals begin in less than two weeks. "If I can do well here in Paris and beat (Djokovic), all the better", Federer said.
John Isner's hopes of also making the London finals received a potentially fatal blow when he was beaten 6-4 6-7 (9) 7-6 (8) in by rising Russian Karen Khachanov.
Austrian Dominic Thiem had to come from behind to beat Borna Coric 6-7 (3) 6-2 7-5 and his reward is a last-eight meeting with America's Jack Sock, a 6-0 6-4 victor over Malek Jaziri.
The 31-year-old Serb can take the top spot in the rankings from Rafael Nadal if he wins a record-extending fifth title in the French capital.