Augustin, 19, had put the visitors 2-0 by half-time and Celtic forward Moussa Dembele made it three near the end.
France finished second in Group Three behind Macedonia but they have not made the play-offs.
Jim Magilton's Northern Ireland ended the campaign bottom of the group with two points from their 10 matches.
Paris St-Germain striker Jean-Kevin Augustin scored twice as France beat Northern Ireland in Tuesday's European Under-21 Championship qualifier.