The win, plus last week's drawn match with champion Auckland City Youth, gives the Dunedin-based team a fine start to the competition, despite early morning starts and double flights, to get to Napier for a noon kick-off.
''We needed a good warmup to overcome the staleness that comes from sitting for lengthy periods, and things got worse when the keys to our dressing room were lost, and there was another delay before we could get the lads outside running,'' manager Richard Kerr Bell said.
In the early stages, Southern looked lethargic, with the home team confidently pushing forward seeking an early advantage. Keeper Josh Dijkstra made a couple of critical saves in that period.
But within 15 minutes it was Southern which seized the initiative with a well-worked goal, from clever passing between Cody Brook and Lewis Jackson which allowed Jackson to calmly shoot his side into a 1-0 lead.
Hawkes Bay continued to press, but the Southern backline of Tyrell Barringer-Tahiri, Keegan Taig, Mitchell Carter and Matt Mitchell showed composed defensive qualities.
Southern again punished the Bay with an attacking break that saw Jackson grab another goal, as a Rahan Ali pass split the home defence, and coach Kevin Scoullar roared approval as his side went 2-0 ahead.
The second half had Southern playing into a decent breeze, but Scoullar's strategy, that produced steady defence yet created 10 shots with seven on target, was counterattacking at its best.
Ali and Brook again breached the opposition with good buildup play and a shot on target, then Matt Kelly and Jackson also tested the home keeper.
Hawkes Bay desperately pushed forward and had Southern under pressure, coach Scoullar brought on quality substitutes. Bob Cox replaced Riley Anderton, Kelly went off and speedster Jeremy Fong took the field, and Rupert Mark replaced Ali.
However, the Bay pulled a goal back, and pressed forward. Under pressure, Southern defended well, and hit back when Cox was provider for Ali to score for a 3-1 lead it refused to relinquish.
Undefeated, with four points in the bag, Southern now looks forward to three home games.