The Manchester United playmaker pulled out of the contest just an hour before kick-off in Saitama.
The Japan Football Association (JFA) said Kagawa felt a slight twinge in his lower back during training. He thought he would be able to shake it off, but at the last minute coach Alberto Zaccheroni decided not to risk his superstar.
Japan went on to win the Group B encounter by 1-0, with Shinji Okazaki finding the back of the net in the 25th minute of play.
After four games, Japan have maximum 12 points and the group over Australia, which will be in action later tonight.
Meanwhile, Manchester United manager Sir Alex Ferguson will be keeping a close on Kagawa when he returns to Old Trafford as he remains a vital part of his team home Barclays Premier League clash against Wigan Athletic on Saturday.
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