Gouiri scored in the 13th and 71st to lift the former champions into the knockouts, while Japan found a consolation goal through Taisei Miyashiro in the 73rd minute at the Indira Gandhi International Stadium.
Japan, though, still are in contention from Group E having hammered Honduras 6-1 in their tournament opener.
The first goal came when Gouiri unleashed a right-footer off from the left side of the box off a Maxence Caqueret assist.
The Olympique Lyonnais youngster opened the scoring on the 13th minute, as he sent a shot through the legs of Japan goalkeeper Kosei Tani.
Despite falling behind, Japan made their way back into the contest and had created chances.
The best of those opportunities was a free-kick from Keito Nakamura, which took a big deflection off the France wall and flew just wide.
At the other end, Caqueret was unlucky not to see a long-range strike hit the target before the break.
The second France goal prompted a reply for Japan, who reduced the deficit through a Taisei Miyashiro penalty.
After that, the French held on for a second straight win in the competition.
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