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Japan took the lead through Daizen Maeda in the 56th minute before Anthony Elanga equalised for Sweden six minutes later.
Japan booked their place in the knockout stage by finishing second in Group F with five points, behind group winners the Netherlands on seven points after their 3-1 victory over bottom-placed Tunisia, who ended the group stage without a point.
Sweden finished third in the group with four points but secured progression to the knockout rounds as one of the eight best third-placed teams. Their goal difference (seven scored and seven conceded) guarantees qualification regardless of the remaining results in the final round of group-stage matches.
Japan will face Brazil in the round of 32 in Houston on 29 June.