The 29-year-old midfielder topped the annual poll of African national team coaches and technical directors to add to the award he won in 2011.
Toure played a pivotal role for both club and country, helping Ivory Coast to the African Nations Cup final in February and then playing a big part in taking Manchester City to the Premier League title in a dramatic season finale.
"Toure's immense contribution in helping Manchester City win their first domestic championship in 44 years saw him pick up Africa's most prestigious individual award," said the citation from the Confederation of African Football, who did not release the tally of votes.
He was also a goal scorer in August's FA Community Shield against Chelsea, won 3-2 by City, and helped the Ivorians easily past a strong Senegal side in Nations Cup qualification in September and October.
Voters picked him ahead of sentimental favourite Drogba, whose dramatic celebrations after converting the decisive penalty for Chelsea against Bayern Munich in the Champions League final were among the abiding images of the footballing year.
Winning the Champions League completed a full sweep of trophy success at club level with Chelsea for Drogba but also heightened the drama of just three months earlier when he missed a penalty for the Ivory Coast in the Nations Cup final.
Drogba led his side on a seemingly unstoppable march to the final in Libreville, where they were runaway favourites, but he ballooned over the crossbar a second half penalty that would have won Ivory Coast a prize that has consistently eluded them.
Instead Zambia went on to win in post-match shootout although Drogba, who signed a two-and-a-half year deal with Chinese side Shanghai Shenhua in June, won praise for bravely again stepping up to take a kick and scoring.
Drogba's other achievement of the year was to become the first player to score in four separate FA Cup finals when Chelsea beat Liverpool at Wembley.
Third in the voting was Cameroon midfielder Alex Song, whose elevation to the trio of finalists was unexpected after a year of turmoil for the national side and no success at club level with Arsenal before he moved to Barcelona.
The award was made at the annual CAF gala in Accra, a rambling affair filled with foibles including the incorrect announcing of a winner of one of the other minor awards.