It will be the first time the world number two has missed the event in Florida, which he has won twice, since 1999.
Federer, who from next year will be exempt from ATP World Tour Masters 1000 commitments due to the milestones he has reached during his career, can now pick and choose which events he attends.
The Swiss will also skip Monte Carlo and his home tournament in Basel, an event at which he used to ball boy.
The 31-year-old will, naturally, play at all four Grand Slam events - in Melbourne, Paris, Wimbledon and New York.
Federer's 2013 schedule:
Australian Open, Melbourne
ABN AMRO World Tennis Tournament, Rotterdam
Dubai Duty Free Tennis Championships, Dubai
BNP Paribas Open, Indian Wells
Mutua Madrid Open, Madrid
Internazionali BNL d’Italia, Rome
Roland Garros, Paris
Gerry Weber Open, Halle
Rogers Cup, Montreal
Western & Southern Open, Cincinnati
US Open, New York
Shanghai Rolex Masters, Shanghai
BNP Masters, Paris