After a goalless first half, Japan struck twice in seven minutes after the interval to take full control of a gripping last-16 tie in Rostov-on-Don on Tuesday (NZST).
Genki Haraguchi and Takashi Inui scored stunners as Japan looked set to reach the first FIFA World Cup quarter-final in its history.
But, instead, Belgium became the first team to come from two goals down to win in a World Cup knockout game since 1970 and will now face five-time winner Brazil on Saturday (AEST).
Jan Vertonghen's looping header somehow beat goalkeeper Eiji Kawashima and Belgium's aerial power started to tell when Marouane Fellaini thumped home Eden Hazard's brilliant left-wing cross.
Keisuke Honda almost beat Thibaut Courtois with a free-kick in injury time but a clinical Belgium counter-attack, which ended in Thomas Meunier setting up Chadli for a simple finish, broke Japanese hearts.