In bitterly cold conditions at the McMillan Hockey Centre, the Storm could only muster one goal by Polly Inglis in the loss.
After opening the national championships with a 4-0 loss to Canterbury last weekend, it was the second consecutive loss by four goals for the home side.
''Not ideal. We didn't look after possession,'' coach Rod Rzepecky said after the match.
''We were coughing it up through pressure on our back three ... and it cost us big time.''
After a goalless first quarter, the visiting side opened the scoring five minutes after the break through Kirsten Pearce, after the Storm failed to clear the ball from its own circle.
She pounced on the loose ball and fired past Ginny Wilson with a reverse stick shot.
Kathryn Henry made it 2-0 four minutes later when she weaved into the circle and calmly slotted the ball into the back of the goal.
Southern looked rattled early in the second half, and gave away a heap of possession through poor passes.
As a result, Harbour enjoyed a wealth of territory and possession and scored two third quarter goals through penalty corners.
Erin Goad made it 3 0 with a tidy deflection from a penalty corner almost immediately after the break, while Pearce scored her second a couple of minutes later, when she swept in a penalty corner.
The home crowd finally had something to cheer about just before the end of the quarter, when Inglis fired home from a tight angle.
However, North Harbour scrambled in another goal through Katy Symons from a penalty corner early in the final quarter to put the game to bed.
Rzepecky said it was frustrating to concede three goals from penalty corners, something the team had talked about before the match.
''We talked about being physical and aggressive in there, but their execution from their penalty corner unit was pretty solid. So credit must to go Harbour. I thought they were pretty slick,'' he said.
''Unfortunately, we didn't match them with the intensity we needed to. At times we were good - we scored a really good team goal - but in the end we weren't good enough.''
The Storm will now have a few days off before heading to Whangarei for the remainder of the competition on Friday.
Its next game is against the Central Mysticks on Saturday.
In yesterday's other games, Northland beat Auckland 3-0, Midlands downed Central 3-1 and Canterbury defeated Capital 4-0.
