Emiliano Boffelli scored the only try and kicked 11 points, Nicolas Sanchez adding a late penalty, to reward the Pumas' domination at the Stade Geoffroy Guichard after their initial defeat by England.
Samoa, who had Duncan Paia'aua sin-binned in the first minute, threatened a comeback with Sama Malolo's late converted try adding to Christian Leali'ifano's penalty, but it was too little, too late.
England lead Pool D with nine points from two games, four points ahead of Samoa and third-placed Japan with Argentina in fourth place on four points.