Ogier still secured the maximum three bonus points for Sunday's final power stage while Latvala took one.
Latvala led all but one of the 18 stages in the Alsace region on his way to a first win on asphalt, with Norwegian Andreas Mikkelsen finishing second in the other Volkswagen for his best world rally championship result.
Britain's Kris Meeke was third for Citroen.
Ogier has 217 points to Latvala's 190 with two rounds remaining in Spain and Britain.
(Reporting by Alan Baldwin, editing by Toby Davis)
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