The result Wednesday night secured Italy a place in the semi-finals alongside Brazil while eliminating Japan and Mexico from the tournament, reports Xinhua.
CSKA Moscow midfielder Keisuke Honda and Manchester United midfielder Shinji Kagawa gave Japan a dream start before Italy wrested the lead via Daniele De Rossi, Mario Balotelli and an own goal from Atsuto Uchida.
Shinji Okazaki drew the Asian champions level before De Rossi's goal against the run of play broke Japan's spirit.
Honda had opened the scoring at Arena Pernambuco when he converted a 21st-minute penalty after Gianluigi Buffon brought down Okazaki in the area.
Kagawa doubled the lead when he held off two defenders with his back to goal before turning and, in the same motion, firing a spectacular volley past Buffon.
But just when Japan looked set to take control, Italy regained their composure.
Roma midfielder De Rossi reduced the deficit just before halftime, arrowing a header past Eiji Kawashima following an Andrea Pirlo corner kick.
Schalke defender Uchida gifted the Azzurri their second goal when he deflected an Emanuele Giaccherini cross into his own net just after the interval.
Balotelli then gave Italy the lead from the penalty spot after Argentinian referee Diego Abal ruled that captain Makoto Hasebe had handled the ball in the area.
But Japan rallied again as Okazaki nodded in a Yasuhito Endo free-kick in the 69th minute.
Honda's dangerous shot after a jinking run was then palmed away by Buffon before Okazaki and Kagawa were denied by the woodwork.
It was just the break Italy needed.
Cesare Prandelli's team regained the lead four minutes from time when De Rossi's perfectly weighted pass released Claudio Marchisio, whose precise cross from the right gave Giovinco an easy tap-in.