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It was a half of few chances, but Mexico almost went ahead right before the break as Andres Guardado's diving header came back off the post.
Mexico regrouped as the stronger side and came out fighting, with Hernandez opening the scoring inside 10 minutes of the restart having finished Guardado's fine cross.
In the 67th minute Hernandez doubled his and Mexico's tally. It was typical Chicarito as he reacted quickest to a near-post flick-on to head in from close range.
As Mexico looked likely to hold on to the lead, Shinji Okazaki gave Japan late hope, firing in Endo's low cross from close range.
However, they were unable to grab the equaliser and Mexico finished third in the group following Hernandez's late penalty miss.