His decision almost ensures Rafael Nadal will finish atop the ATP rankings with Federer at No. 2. Nadal needs just one win in Paris to finish No. 1.
"My body is asking for a break," Federer told reporters on Sunday after defeating Juan Martin del Potro to win in Basel, his hometown. "Basel takes a lot out of me emotionally. I had five matches in six days. I feel sorry and sad for Paris.
"I love to play at Bercy. ... It's a tough one but they have to understand that it's for the cause of staying injury-free and healthy."
The 36-year-old Federer has not played the Paris tournament since 2015. He last won it in 2011.
Federer has won an ATP-leading seven championships this season and also has won the Australian Open and Wimbledon. He has 19 Grand Slam titles.