The 22-year-old Moroccan netted his fifth goal of the campaign with a fine solo effort as Schalke moved up to sixth place on 18 points, four behind leaders Borussia Moenchengladbach.
Augsburg managed to score twice in the first half, once with captain Daniel Baier to take the lead in the 38th minute and another with Stephan Lichtsteiner's glancing header for an own goal on the stroke of halftime that brought the Royal Blues level.
Alfred Finnbogason's well taken penalty, awarded for a handball, put the hosts again in front on the hour but Schalke once more responded with Ozan Kabak's darting header from a Daniel Caligiuri free kick 11 minutes later before Harit snatched the late winner.
Borussia Moenchengladbach lead the standings with 22 points after their 2-1 win at Bayer Leverkusen on Saturday.
Borussia Dortmund's 3-0 victory over VfL Wolfsburg lifted them to second place on 19, leaving Bayern a point behind after slumping to a 5-1 defeat at Eintracht Frankfurt. RB Leipzig and Freiburg are also on 18.