The 31-year-old Ivory Coast international also won in 2011 and 2012.
Nigeria’s John Obi Mikel was second and Didier Drogba of Ivory Coast finished third.
“I thank my family for their support and also congratulate John Obi Mikel, who also deserved this award,” said Toure, who was a key player for both club and country last year.
Egyptian legend Mohamed Aboutrika beat compatriot Ahmed Fathy and Sunday Mba from Nigeria to win the best Player based in Africa.
It was a fitting send-off gift for the 35-year-old Al Ahly star, who has announced his retirement from the game.
Ahly were also rewarded as the Club of the Year ahead of CS Sfaxien of Tunisia and South Africa’s Orlando Pirates after they won an eighth CAF Champions League trophy.
Nigeria scooped several awards to underline a very successful year with coach Stephen Keshi voted Africa’s best coach, while the Super Eagles were the best national team after they won a third Africa cup of Nations in February and qualified for a fifth World Cup.
The country’s Under-17 team were picked as the National Youth Team and Kelechi Iheanacho, who was voted the MVP of the 2013 Under-17 FIFA World Cup, received the Most Promising Talent award.
The list of winners of the 2013 CAF Awards:
African Footballer of the Year: Yaya Toure
Best African-based Player: Mohamed Aboutrika
Coach of the Year: Stephen Keshi
Most promising Talent: Kelechi Iheanacho
National team of the Year: Nigeria
National Youth Team of the Year: Nigeria Under-17
Club of the Year: Al Ahly of Egypt
Referee of the Year: Haimoudi Djamel
Legends of the Year: Bruno Metsu, Jose Faria
Africa XI: Vincent Enyeama – Ahmed Fathi, Mehdi Benatia, Kevin Constant – John Obi Mikel, Yaya Toure, Mohamed Aboutrika, Jonathan Pitroipa – Emmanuel Emnike, Asamoah Gyan, Pierre-Emerick Aubameyang
Coach: Stephen Keshi