The best match of the tournament ended in devastating fashion for the Asian nation, which let a two-goal lead slip to lose, and in the process seal its elimination
Needing a win to stand a chance of making the last four, Alberto Zaccheroni's men got off to an incredible start, racing into a two-goal lead through Keisuke Honda's penalty and Shinji Kagawa's neat finish.
But a spectacular 11-minute turnaround either side of halftime saw Italy score three to retake the lead, through Daniele de Rossi's header, Atsuto Uchida's own goal and Mario Balotelli's penalty.
Shinji Okazaki then drew Japan level with 21 minutes remaining, but despite a late rally by the Samurai Blue, they were finished for good with four minutes remaning by Sebastian Giovinco's strike, as Italy joins Brazil as Group A's representatives in the last four.
Cesare Prandelli made two changes to the side that beat Mexico 2-1 Sunday, with Christian Maggi and Alberto Aquilani coming in for Ignazio Abate and Claudio Marchisio, while Japan saw Ryoichi Maeda return to lead the line.
And the Jubilo Iwata forward could have made an instant impact after only five minutes, but did not direct his header well from Kagawa’s inch-perfect cross, as Gianluigi Buffon saved comfortably.
Zaccheroni’s men were the brighter side throughout the opening exchanges, and with 20 minutes on the clock, were handed the chance to take the lead when Buffon conceded a penalty after upending Okazaki inside the area.
The keeper escaped with only a yellow card, but was powerless to stop Honda’s low strike to the bottom right corner from 12 yards, despite guessing correctly.
Balotelli was then incredulous that he was denied a penalty of his own after tussling with Maya Yoshida, but in truth, it was an unlikely claim for an increasingly desperate Italy, which was struggling to match the intensity of Japan.
And with just over half an hour gone, the Samurai Blue made their superiority count once again. Italy failed to clear a ball into the box, and Kagawa was quickly on it, planting a fine half-volley into the corner.
In fact, Honda could have made it 3-0 moments later from a free kick, but Buffon was on hand this time to make a smart double save to keep the deficit at two.
Italy finally began to wake up as the half neared its end, and it was Andrea Pirlo, as ever, leading its revival, coming close with a wicked free kick that whistled just over the top.
But the Juventus midfielder was deadly accurate with his delivery from a corner in the 41st minute, picking out De Rossi at the near post, who thumped home with his head.
Japan was stunned, and nearly capitulated at the end of the half when Emanuele Giaccherini’s bit of trickery saw him evade his marker but crash the ball off the frame of the goal.
But its resistance lasted little more than five minutes after the restart, as Giaccherini’s pass across the face of goal to Balotelli was reached first by Uchida, who ended up turning the ball into his own net.
And two minutes later, it got even more painful for Japan, when Makoto Hasebe conceded a penalty for an extremely harsh handball call, from which Balotelli, as ever, converted coolly from the spot to put Italy in front for the first time.
Eiji Kawashima was then called into action twice in quick succession to deny Giovinco and De Rossi, and his efforts were rewarded at the other end in the 69th minute, when Okazaki headed home from Yasuhito Endo’s free kick.
But not for the first time, Japan was left cursing its luck when an almighty scramble inside the box saw Okazaki hit the post, before Kagawa's headed follow-up bounced off the floor and smacked off the crossbar.
And in the 86th minute, just when Zaccheroni's men looked like stealing the winner, Italy put the game to bed when De Rossi released Marchisio, who in turn squared for Giovinco to stab high into the back of the net.
Yoshida then had a goal disallowed for offside, and Buffon was forced to tip away from Honda as Japan fought or their lives, but time was no longer on their side as the final whistle signalled the end of its campaign.