The win puts Belgium into the quarterfinals, setting up a mouth-watering clash with Brazil in the last-eight. And despite dominating possession, Belgium failed to create many other quality chances while Japan looked risky throughout the first half on the counter-attack.
Fox Sports timed the counterattack at 9.9 seconds.
Chadli broke Japanese hearts when he completed a move on the break, with all five goals coming in the second half of an enthralling last-16 match in the Rostov Arena on Monday.
Gareth Southgate admits knives will be out if England lose to Colombia
But star-studded Colombia are sure to prove a far tougher test than Belgium's back-ups in Moscow. In playing terms, a deflating night did exactly the opposite", wrote Matt Dickinson in the Times.
Belgium's two-goal comeback is the first in the knockout stages of the World Cup since 1970, and may give them the belief that they can go all the way, although they will have to go through Neymar and co. next.
Nearly immediately Eden Hazard struck the post for Belgium, but in their next attack Japan doubled their score, when Shinji Kagawa back-heeled to Inui on the edge of the area, and he had time to tee up a shot inside the keeper's left post.
Japan were dominating a bewildered Belgium side who were forced to make a double change as Nacir Chadli and Marouane Fellaini replaced Dries Mertens and Yannick Carrasco.
Japan took the lead when they won possession deep in their own half.
Low will keep Germany job regardless of results
Unfortunately they are injured. "Clearly we expected this to be a long tournament for us, we expected to be here for a lot longer. Elsewhere, Mexico fans carried South Korean fans aloft through Mexico City's main square in a victory march after the result.
Japan (4-2-3-1): Kawashima; Sakai, Shoji, Yoshida, Nagatomo; Hasebe, Shibasaki; Haraguchi, Kagawa, Inui; Osako.
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.
Chaldi, who came on as a substitute in the 65th, decided it in injury time.
Sampaoli planning to use Messi as a false nine against France
France is set to take on Lionel Messi and Argentina as the high-stakes single-elimination round of the tournament soon begins. The opening match of the knockout stage of the 2018 World Cup will kick off in spectacular fashion.