Sean Maitland crossed either side of the break after Damian Penaud's score, before Stuart McInally added a third.
Charles Ollivon's late try could not deny Gregor Townsend consecutive wins.
Adam Hastings, who impressed in place of the exiled Finn Russell, added 13 points with the boot.
Fabien Galthie's side had won their first three games of the Six Nations but a first-half red card for Mohamed Haouas let Scotland seize control.