It was recognition for his part in Bayern's unprecedented Champions League, Bundesliga and German Cup treble.
The Frenchman was the first player from a club other than Barcelona or Real Madrid to make the final three since the award was established by European soccer's governing body in 2011.
Argentina's Messi won the inaugural award followed by Spaniard Andres Iniesta, his Barcelona team mate, last year.
Messi and Real Madrid's Portugal forward Ronaldo had also both made the last three in each of the two previous years.
Image: Franck Ribery
Photograph: Jean Pierre Amet/Reuters