The current world No 1 made his decision - one which means Novak Djokovic will now finish the year at the top of the rankings - after suffering a three-set defeat by Juan Martin del Potro at the Swiss Indoors in Basel on Sunday.
Federer, who skips the event he won a year ago as part of a sweep of the last three events of the 2011 season, said: "I'm not going to Paris, it's too much for me.
"I've already told tournament director Guy Forget. I have some niggling stuff that I want to heal, I don't want to take a chance for London.
"Missing Paris is disappointing. I remember how great it was to win the title a year ago. I had one of the best weeks of my life there in 2011."
With Rafael Nadal also missing after ending his campaign early because of a knee complaint, the Paris field will now be led by Djokovic and US Open winner Andy Murray.
Federer's place in the draw for the Paris Masters has been taken by Romanian lucky loser Victor Hanescu.
He will play Gilles Simon or Marcos Baghdatis in his opening match.