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Keisuke Honda, Yasuhito Endo and Shinji Okazaki were on target for Japan, while Jon Dahl Tomasson pulled one back, nine minutes from time.
The Netherlands warmed up for their World Cup last-16 match against Slovakia with a 2-1 win over a spirited Cameroon courtesy of goals from Robin van Persie and Klass-Jan Huntelaar. Samuel Eto'o scored the only Cameroon goal on 65th minute from penalty.