The 25-year-old Germany stopper, who joined Bayern from Schalke earlier this summer, came top of the annual poll run by sports magazine Kicker and became the first goalkeeper since Oliver Kahn 10 years ago to win the award.
He beat new club-mate Mario Gomez into second place, with Nuri Sahin - recognised for his displays in Borussia Dortmund's Bundesliga-winning campaign before switching to Real Madrid - third.
"This is a huge honour," Neuer told Kicker.
"When I was first told, I thought someone was pulling my leg. I'm totally shocked, especially because it's not every day a goalkeeper wins the award."
Neuer, who helped the Royal Blues win the DFB-Pokal last term and reach the Champions League semi-finals, will be presented with the award at the Allianz Arena ahead of Bayern's opening Bundesliga fixture of the season against Borussia Monchengladbach on Sunday.