Bwalya, who was voted the region's top footballer in 1988 and later went on to become president of his country's football association, said he was pulling out to concentrate on winning re-election to the African governing body's executive committee.
Elections for African places on the new-look FIFA Council will be held at the Confederation of African Football (CAF) Congress in Addis Ababa on March 16, at the same time as the CAF executive committee vote.
Bwalya was initially standing for places on both bodies but told reporters: "I have decided to withdraw from the race, to concentrate on retaining my exco position."
Bwalya was one of three candidates for the place on the FIFA Council reserved for a representative from Africa's Anglophone countries.
His withdrawal leaves a straight fight between Ghana Football Association president Kwesi Nyantakyi and Leodegar Tenga of Tanzania.
Africa has seven places on the FIFA Council, which has been renamed and expanded since Gianni Infantino came to power one year ago.
One place is automatically reserved for the CAF president and another for a female representative. The other five places will be decided in Ethiopia on March 16.
(Reporting by Mark Gleeson in Cape Town; Editing by John O'Brien)
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