In french, instead of using "contrôle de version", I would use "Gestion de version". So for a "version control system" I would use "système de gestion de versions" or even "logiciel de gestion de versions".
"Gestion de version" seems to be the expression widely useused, as a Google search for "gestion de version" and "contrôle de versions" both returnsreturn the same results which points to the expression "gestion de version".
And for the complete expressions, "logiciel de gestion de versions" seems theto be the most common one. "logiciel de gestion de versions" also seems to be the expression that Wikipedia uses (even though that's maybethat may not be the most official source). I'm still looking for an official source but haven't found anything yet.