The Manchester City player beat fellow Ivorian and former Chelsea striker Didier Drogba into second with Cameroonian Alex Song, of Barcelona, in third.
He joined Senegalese forward El-Hadji Diouf, formerly of Liverpool and Bolton, on two victories although he has some way to go to eclipse Cameroonian ex-Barcelona striker Samuel Eto'o who has won four titles.
The Côte d'Ivoire player was crowned at an awards gala in Accra, the capital of Ghana, on Thursday evening after being voted for by the head coaches or technical directors of the national associations affiliated to the CAF.
The giant midfielder appeared to tear up as his name was called at the ceremony in Ghana's capital.
"I have a lot of emotion," he said after climbing the stage to accept the award. "I think this night is so special for me."
When asked about the forthcoming CAF African Cup of Nations, Toure was diplomatic.
He said: "I think this year is going to be tough. I think there's going to be a fight to be at the top," he said after accepting the award.
Toure's second CAF honour came on a night when Drogba, the former Chelsea star now playing for Shanghai Shenhua, was in line for his third win.
Drogba was seeking to take a step closer to Cameroonian Samuel Eto'o's record four trophies but described his fellow Ivorian as a deserving winner who has played with impressive "consistency over the last two years."
"Being in competition against Yaya and Alex was for me very difficult," said the striker. "For me, I don't mind if Yaya wins. I'm very proud."
Song, a 25-year-old up-and-coming midfielder, was nominated for the first time this year, after a good season for Arsenal before his transfer to Barcelona.
African Nations Cup winners Zambia were named team of the year with their coach Herve Renard named coach of the year.
It beat South Africa in the final, the side's second title in a competition often dominated by Nigeria, which has won six times.
It was a night full of awards for Egypt, with Cairo-based Al Ahly named as club of the year after securing its seventh CAF Champions League crown.
The club's star Mohamed Abourtrika took home the award for the best player based in Africa.
Mahmoud El-Gohary provided the fourth Egyptian triumph of the night, winning a Legend award for a range of both club and national titles won during the 74-year-old's long professional of career.