The hometown hero and world number one will miss the chance at possible revenge against Andy Murray after a Shanghai semi-final defeat a week ago as the US Open champion withdrew with back pain before the draw.
It was Murray's second straight Basel pullout after he quit prior to his first match a year ago with a muscle injury.
Murray has not played a match at the venue since his only appearance in 2005 as a teenager.
Federer, as usual, is scheduled for prime-time Monday evening at the St Jakobshalle, the iconic local venue where he got his start in tennis two decades ago as a ballboy.
He will open his title defence against German qualifier Benjamin Becker after French opponent Jeremy Chardy withdrew injured before the start.
Chardy was reported to be suffering with neck pain as he handed over his spot in the draw.
The Swiss world number one stands 2-0 over Becker without the loss of a set.
Federer will be fighting during the week to protect his top season ranking, with pressure on from number two Serb Novak Djokovic, who is taking the week off from competition.
Federer is defending champion's points over the next three weeks after a stunning finish to last season.
The 31-year-old has won five of the last six editions in Basel, defeating Japan's Kei Nishikori in the 2011 final.
Argentine Juan Martin del Potro, chasing a spot in the ATP World Tour Finals in London for which Federer has already qualified, takes the second seeding, ahead of Richard Gasquet of France.
Swiss Stanislas Wawrinka is seeded fourth and begins against Russian veteran Nikolay Davydenko.
Italian Andreas Seppi takes the fifth seeding, ahead of Mikhail Youzhny, Florian Mayer and Viktor Troicki.
Wild cards go to a pair of Swiss players — longtime Federer friend Marco Chiudinelli and youngster Henri Laaksonen.