Southern scored a try in the dying minutes at Bathgate Park to finish ahead of Harbour in a match which ebbed and flowed throughout.
Harbour looked to have secured the victory when halfback Tala Fagasoaia dived over with just five minutes left.
That came after a long stint of pressure by Harbour on the Southern line.
Both teams enjoyed sustained periods on attack but were rather one-dimensional in trying to get the ball over the tryline.
The match was marred by an ugly fight at the end of the first half between Southern hooker Junior Sala and Harbour loose forward Iloa Lihau.
They traded several punches and were rightly red-carded by referee Mitch Will.
The game did not lose its structure after they left, although many players struggled on the rather puggy surface.
Harbour led 12-10 at the break after a nice break by the Harbour backs put Fagasoaia over.
After he scored his second try, Southern managed to get the ball back and piled into the breakdown.
Following several phases, the ball went to the left and fullback Josh Buchan dived over.
Southern had Mike Mafi back at No8 and he made plenty of metres with the ball in hand while lock Axel Hohneck was industrious.
Halfback Josh Walden linked well and Josh Ioane outside him kicked well and was good with the ball in hand.
Harbour lock Hale T-Pole was into everything, prop Aidan Spence got round the field, while first five-eight Joe Collins showed some nice touches.