The Blue Samurai squandered a two-goal lead during the match before Nacer Chadli knocked them out with the final kick of the game.
"I am devastated. Yes we took the lead but we couldn't win," BBC Sport quotes Nishino as saying. "It might have been a very small difference but I felt there was nothing in it.
"Maybe it was my decisions as a coach or my tactics, and we couldn't keep up with Belgium, who upped their game."
Belgium will face Brazil in the quarter-finals of the competition.