Nacer Chadli scored the victor in the fourth minute of added time, finishing a breakaway move to leave Japan's players in tears at the final whistle.
Belgium are going through to face Brazil in the quarter-finals. And despite dominating possession, Belgium failed to create many other quality chances while Japan looked unsafe throughout the first half on the counter-attack.
Fox Sports timed the counterattack at 9.9 seconds.
After a goalless first half, Japan struck twice in seven minutes following the interval to take full control of a gripping last-16 tie in Rostov-on-Don on Tuesday morning (AEST).
Trump to announce supreme court pick on 9 July
Some possible nominees being eyed include Thomas Hardiman, who serves alongside Trump's sister on the Philadelphia-based 3rd U.S. Circuit Court of Appeals, and Raymond Kethledge, a federal appeals court judge who clerked for Kennedy.
Future starts now for Germany after shock first-round exit in Russian Federation
Sweden's Ludwig Augustinsson put his side ahead against Mexico and in return, he sank Germany's hopes of progressing. As the squad lined up for a photo call at Incheon International Airport, most of the crowd seemed happy to see them.
Genius Messi a shining light for Argentina, says Sampaoli
Now, the Soccerbot has digested the film, crunched the numbers and broken down every single player on France and Argentina . The last South American team to beat France at the World Cup were Argentina in 1978.
Belgium very almost responded instantly, with Eden Hazard rocketing a shot off the post just after the reset.
Japan started off their World Cup campaign with a victory over 10-man Colombia as Shinji Kagawa and Inui scored for the Japs to win 2-1 over Colombia.
Unfortunately for Japan, the lead would prove short-lived.
Substitute Fellaini astonishingly drew Belgium level to huge sighs of relief after heading home an excellent Eden Hazard cross to make the scores 2-2.
The Red Devils were still struggling but they pulled a goal back after 69 minutes when Vertonghen looped a header from a high clearance back across goal into the far top corner.