Toure, who has scored 13 goals for club and country this year, was the choice of the BBC’s global audience.
He held off competition from Pierre-Emerick Aubameyang (Gabon and Borussia Dortmund), Victor Moses (Nigeria and Liverpool, on loan from Chelsea), John Obi Mikel (Nigeria and Chelsea), and Jonathan Pitroipa (Burkina Faso and Rennes).
Toure was presented with the award at Manchester City’s Carrington training ground on Monday.
“We are pleased for Yaya Toure that he has finally won the BBC African Footballer of the Year on his fifth nomination for the award,” said BBC Africa’s current affairs editor Vera Kwakofi.
“This shows the high esteem in which he is held by lovers of African football and the respect the fans have for his exploits for club and country.”
Toure now has the chance to complete an awards double having been selected among a 25-man shortlist for the African Football Confederation (CAF) African Footballer of the Year for 2013.
In contrast to the BBC award, Toure has won the CAF equivalent in each of the last two years and winning it for a third consecutive year would see him match the achievement of Cameroon striker Samuel Eto’o, winner in 2003, 2004 and 2005.
The winner of the latest edition is due to be announced at a ceremony in Lagos, Nigeria, on January 9.