Being recognised by his peers eased the pain after his team Yokohama F Marinos blew the chance of clinching the league title with defeat to Kawasaki Frontale in their final game on Saturday.
Nakamura, now 35, also collected the award in 2000 in his first spell with his home-town club.
Nakamura - named PFA Scotland Player of the Year in 2007 following an outstanding campaign at Celtic - said: "I know what it takes to have a good season: I had it at Celtic too, so I understand that feeling.
"I know you can't do this without having very talented teammates, coaches and, of course, great supporters.
"All those things come together and that's when it's possible to receive this kind of prize."