Waters made two free throws with 3:02 left in regulation to give Alabama State a 56-53 lead. Southern's Adrian Rodgers tied the game with a 3-pointer with 57 seconds remaining and neither team made another shot, forcing overtime.
Rodgers made a basket at the 3:03 mark of overtime for a 59-57 lead, but the Jaguars went scoreless the rest of the way.
Wendell Lewis had 15 points and 10 rebounds to help Alabama State (11-5, 7-0 Southwestern Athletic Conference) win its eighth straight game. Waters was 4 of 17 from the field, but went 9 of 10 from the free throw line.
Rodgers finished with 21 points for Southern (9-13, 6-2). The Jaguars had their five game winning streak snapped.