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 used, as a Google search for “gestion de version” and “contrôle de versions” both return the same results which points to the expression “gestion de version”.
And for the complete expressions, “logiciel de gestion de versions” seems to be the most common one. “logiciel de gestion de versions” also seems to be the expression that Wikipedia uses (even though that may not be the most official source). I’m still looking for an official source but haven’t found anything yet.
In computer and software industry we use “gestion de configuration” even if I admit that “gestion de version” is better. It appears in a great lot of French resumes, though.