Bwalya on Friday said "let us put this incident behind us for the good of football."
Two Zambian players were hurt when two youths threw stones at the bus as it left Soccer City stadium in Soweto following a 1-0 win over South Africa on Wednesday. Goalkeeper Kennedy Mweene needed stiches in his head after bus windows were shattered.
Gallery: Bafana v Zambia
Video: South Africa v Zambia
Police apprehended the boys, aged 12 and 13, who were released for counseling.
South African Football Association president Kirsten Nematandani apologised for the "embarrassing behavior" ahead of the country's hosting of the African Cup of Nations early next year.