The Magpies win was spearheaded by No 8 Lafaele Faamoe, blindside flanker Sam Crompton and lock Tom Franklin who dominated possession.
Wing Mike Henty showed his blistering speed to score two first half tries.
Southern went to the break with a 22-0 lead and added three more tries and 26 more points in the second spell to retain their second spot on the points table.
Kaikorai were second bottom two games ago but they have moved steadily up the ranks with wins over top ranked teams Dunedin and Varsity A in the last two games.
They scored a bonus point, 30-8, win against the students at Bishopscourt today.
Taieri remain at the top of the competition after scoring six tries when beating Pirates 34-28.
Pirates No 8 Solomon T-Pole received a red card and Pirates played with just seven forwards in the second spell when they outpointed Taieri 22-19.
The scores were: Kaikorai 30, University A 8; Dunedin 33, Green Island 14; Taieri 34, Pirates 28; Southern 48, Harbour 5; Alhambra-Union 19, Zingari-Richmond 8.
