Belgium, moreover, did so with two goals from substitutes, the first time this has ever ocurred in World Cup history.
With centre back Vincent Kompany back in the line-up for the first time since picking a groin strain in a warm-up game, Belgium had looked safe at the back but uninspired up front.
Lukaku, who was marked, left it for Chadli to tap home and cap Belgium's stunning win right before the final whistle.
The Japanese were ahead soon after the break, though, when Haraguchi beat the offside trap and ran into the area to beat Courtois with a cross-shot in the 48th minute.More news: Melania Trump makes surprise visit to US-Mexico border
Nacer Chadli scored with the final kick off the game to complete a remarkable Belgium comeback in their 3-2 win over Japan in the last 16 of the World Cup this evening.
Vertonghen was guilty of some sloppy defending for Japan's opener, and he was a little fortunate to pull one back with a header that looped over goalkeeper Eiji Kawashima.
Belgium very almost responded instantly, with Eden Hazard rocketing a shot off the post just after the reset.
At the other end, Courtois saved Keisuke Honda's wickedly curling free shot which led to the winning goal.
De Bruyne advanced the ball with a attractive push, making a flawless lead pass to Jan Vertonghen with room to run.