The prolific Borussia Dortmund forward, who received 143 votes to four-time winner Toure's 136, is the first player from the central African country to win the award.
His accolade comes despite a year without trophy success. He was captain of the Gabon team eliminated in the first round of the African Nations Cup finals in Equatorial Guinea at the start of 2015 and his club finished seventh in the Bundesliga last season.
But he did score 29 Bundesliga goals in 2015, including 18 this season plus a further seven in the Europa League. He is the first Bundesliga-based player to win the annual award first introduced in 1970.
“His potency in front of goal has seen him become one of the most recognisable strikers in Europe this season,” said his citation.
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“I thank the people of Gabon, this award is for them. I want to thank my team mates in the national team and also at Dortmund. It is their work that helps me to score goals. For the parents of the youth of Africa, please give your kids a chance to realise their dreams,” Aubameyang said in his acceptance speech.
The 26-year-old is the second player born in Europe to win the award after Frederic Kanoute, the Parisian-born Mali international.
Aubameyang’s father was captain of Gabon and played professionally in France. His mother is Spanish, he was born in France but raised in Italy.
The African Footballer of the Year is decided by a vote of coaches or technical directors of all Africa's national teams.
Toure had won the award for an unprecedented four years in succession from 2011-2015 and was the favourite for a fifth after captaining Ivory Coast to the African Nations Cup title.
Ghana international Dede Ayew, who left Olympique Marseille in France for Swansea City in mid-year, was third with 112 votes. His father Abedi Pele won the award three times from 1991 to 1993.
(Reporting by Mark Gleeson; Editing by Justin Palmer; mark.gleeson@thomsonreuters.com; +27828257807; Reuters Messaging: Reuters Messaging: mark.gleeson.thomsonreuters.com@reuters.net)
