Southern snapped Harbour's 14-game winning-streak with a 24-22 victory at Bathgate Park but the visitors picked up a crucial bonus point which saw them secure the Gallaway Trophy.
Southern led 21-5 at halftime, but Harbour stormed back into the lead before Bryce Hosie knocked over a later penalty to win the game for the home side.
In other games, Taieri beat Dunedin 46-8. University A beat Green Island 60-24.
Zingari-Ricmond trumped Alhambra-Union 34-17 and Kaikorai beat Pirates 46-31.