The winning goal was well worth three points as defender Sam O'Regan hammered in a 35th-minute free kick that left Southern keeper Liam Little clawing at fresh air.
Little replaced regular Tom Batty and justified coach Mike Fridge's decision as he made several very good saves, the best from a powerful close-range header by Federico Marques. But Southern coach Fridge admitted it was a poor performance from his side.
''In the first half we were poor and, although there was improvement in the second spell, there was more huff and puff than clear shots at goal,'' he said. WaiBOP emerged as a well-balanced competitive side that might have been placed higher in the Premiership but for an administrative error that cost coach Peter Smith three important competition points.
''It was a frustrating error, but today's performance has put us back on track.
''We tried to approach the match as professionally as possible. Brought the squad down last night to Dunedin, got in a good night's sleep, and had a light practice run to get used to local conditions,' he said.
Smith got what he wanted as his team started well, winning good possession and passing the ball around, with former international Chad Coombes and Alexis Varela setting up attacks.
In contrast to many teams that almost over-pass, WaiBOP also had a clinical cutting edge around Southern's penalty area, with reverse passes and one-twos creating space and opportunities.
Southern's playmakers, Victor Da Costa and Eder Franchini Pasten, were less effective, although both worked hard, and Pasten launched a rare couple of shots that might have affected the result.
Fridge rang the changes at halftime bringing on big Jude Fitzpatrick and striker Alistair Rickerby, and later another front runner in Taylor McCormack.
Fitzpatrick paid immediate dividends with no-nonsense defending, and in attack he added effective height and power as Southern earned many corners and free kicks and also used Tom Jackson's long-throw capability.
But the WaiBOP defence, well led by team captain Aaron Scott and his backline of Mark Jones, O'Regan and Fergus Neil, gave little away, and keeper Danyon Drake had safe hands.
However, the keeper's feet were less capable and, in one mind-numbing incident, he hacked a clearance into the back of Rickerby as the Southern attacker chased in and the ball rebounded off Rickerby's back and headed towards the empty goal mouth.
It was a hypnotic moment worthy of TV bloopers as spectators craned and watched the ball spin in slow motion and curl goalwards but it lacked enough pace to hit the net, and was cleared off the goal line.
Southern has a bye next week which would ordinarily have narked coach Fridge, but since key players Pasten and Jackson collected injuries in the second half, perhaps the down time will help their recovery.
