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 had made the knockout stages despite being tied on points with third-placed Senegal in Group G as they had better Fair Play points than the African side.
Kick-off is 7pm Nigerian time.
Japan shocked their much-fancied opponents early in the second-half when midfielder Genki Haraguchi gave his side the lead in the 48th minute against the run of play.
And Vertonghen's strike was definitely that, a looping header from nearly outside the box, and intentional or not, Belgium were level in the 69th minute.
Here are the possible players who can be part of Belgium team today.
Since Gerd Muller scored 10 goals at the 1974 World Cup for West Germany, five or six goals have usually been enough to claim the top scorer's award at the tournament - with a couple of notable exceptions, including Ronaldo's eight in 2002.
Teams such as Brazil or Mexico could await them in the quarterfinals, while France or Uruguay loom further down the line.
Relieved Belgium manager Roberto Martinez saluted his side's resolve. Used possession well in the biggest game of his career to date, though perhaps should have been a little more aggressive as Belgium came back.
With players like Eden Hazard and Romelu Lukaku at his disposal, Martinez's team have more than enough quality to match their achievement at the last World Cup and secure a place in the quarter-finals, where Brazil could await.
"Belgium is a top-three team (in the Federation Internationale de Football Association rankings)".
Head coach Akira Nishino, meanwhile, revealed he has held lengthy conversations with goalkeeper Eiji Kawashima after some uncharacteristic mistakes in Japan's first two matches of the group stage. "However, Japan can now play with confidence".
So Belgium are supposedly on the "tougher" side of the World Cup bracket.
Takashi Inui calmly collected Shiji Kagawa's layoff near the box and curled one past Courtois to leave the Belgian Red Devils shellshocked.
Fellaini headed home Hazard's cross off a corner, and as Japan exhausted, the Red Devils began to dominate.