The Germany international, a World Cup winner last year, finished third to Real Madrid star Cristiano Ronaldo and Barcelona gun Lionel Messi.
Klinsmann had hoped countryman Neuer would win the award, and said Germany coach Joachim Low deserved his World Coach of the Year prize.
"I think it's a no-brainer that Joachim Low is the coach of the year worldwide, because he won the World Cup. He did an outstanding job," Klinsmann said.
"I was a bit sad for Manuel Neuer because I thought he played outstanding. But at the end of the day, the most important title you can win in your career is the World Cup.
"When you talk about players like Cristiano Ronaldo or Messi, you talk about world class players and you wish them all the best.
"I was voting for Manuel Neuer, I hoped for him but unfortunately he didn't get it."
