Portuguese Cristiano Ronaldo won the award on Monday for the second year running and third time in total.
The Real Madrid forward polled more than twice as many votes as his bitter rival and four-time winner Lionel Messi, who only just edged Bayern Munich's Neuer into third place.
Neuer, who was outstanding at last year's World Cup in Brazil and also helped Bayern clinch a domestic double, has let in just four goals in 17 league games so far this season.
"I think this is unfair," said Germany's former World Cup-winning captain and coach Franz Beckenbauer. "It seems that in this vote success does not count as much as appearances."
"Keepers are in a difficult spot. People want to see goals, not the people stopping the goals."
Germany had been hoping for a clean sweep of awards after coach Joachim Loew won coach of the year award while VfL Wolfsburg coach Ralf Kellermann was voted best coach in women's football.
Wolfsburg's Germany midfielder Nadine Kessler was voted female player of the year.
"I am a bit disappointed for Manuel," Loew told reporters. "Because at the World Cup Manuel showed a completely different goalkeeping game and that is something that has never happened before."
Neuer was voted goalkeeper of the year in 2014 after a string of outstanding performances at the World Cup, where he also ventured out of his box more often than others in the past.
But he did not even get support from all his Bayern teammates with Robert Lewandowski, the Poland striker, voting instead for the Portuguese.
"It was a mistake from me to vote for Ronaldo," Lewandowski told reporters. "Today I would vote for Manuel but I voted some time in August. I would vote differently today."
For the easy-going Neuer, however, the evening was a success even without the trophy.
"I am leaving this building with a big smile on my face. It was a winning day for me and it was a success just being in the top three," he said. "2014 was a year with a lot of success and it will forever stay in my memory."
(Reporting by Karolos Grohmann, editing by Alan Baldwin)
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