Federer says "it's better that I announce now" that he'll miss the Sept. 13-15 series at home following the U.S. Open.
The 31-year-old Federer previously said he would schedule more breaks for family and recovery time this year. But he was criticized at home for being unclear about his Davis Cup plans before skipping a first round loss against the Czech Republic in February.
Federer says he spoke with Swiss federation president Rene Stammbach at the Madrid Masters this month, and again by telephone before making his decision.
Switzerland will host Ecuador on indoor hard courts in Neuchatel. The winner stays in the 16-nation world group in 2014.