The Ivory Coast international held off competition from compatriot Didier Drogba and Cameroon’s Alex Song, who plays for Barcelona.
The 29-year-old was adjudged winner of the continent’s highest individual football prize for 2012 by coaches of national teams affiliated to the Confederation of African Football (Caf).
“This night is so special for me,” Toure said after receiving the prize in Ghana’s capital, Accra on Thursday. “Thanks to all of you. Even my captain is here today. Thanks to everyone and we are happy for this award.”
The Ivorian was in powerful form for Ivory Coast in the Africa Cup of Nations earlier in the season, and was unfortunate to see his side lose in the final to Zambia, in a penalty shootout.
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Toure returned to his club, however, in inspired form and helped City to a first Premier League title in 44 years - a double at Newcastle in the penultimate game of the season proving vital to the cause.
The midfielder has taken that form over to 2012-13 and has scored six goals in 23 appearances so far this season, as well as captaining the side in Vincent Kompany's recent absence.
Winners of the other categories are:
National Team of the Year – Zambia
National Women’s Team of the Year – Equatorial Guinea
Club of the Year – Al Ahly
Fair Play Award – Gabon Supporters Union
Coach of the Year Award – Herve Renard
Most Promising Talent Award – Mohamed Salah (Egypt)
Women’s Footballer of the Year – Genoveva Anonma (Equatorial Guinea)
Referee of the Year – Gamal Hymoudy (Algeria)
Caf Legend of the Year Award – Rigobert Song (Cameroon) and Mahmoud El Gohary (Egypt)
African Player of the year – Based in Africa - Egypt's Mohamed Aboutreika - Al-Ahly
Zambia's Rainford Kalaba - TP Mazembe
Zambia's Stoppila Sunzu - TP Mazembe