Auckland City poked in the winner in the 82nd minute following a melee in front of goal to seal the win in Invercargill.
But the home side produced a gutsy defensive effort that pleased coach Paul O’Reilly.
"We defended really well and in the first half we looked like we might cause a threat with the counterattack," O’Reilly said.
"We did not turn over too many chances but in the second half they put a bit more pressure on us.
"We worked really hard but conceded a late goal, unfortunately. We had one or two half chances after that but couldn’t get back into the game.
"But I’m really happy with the performance but obviously disappointed with the 1-0 defeat."
An early corner to competition leader Auckland City brought out the best in Southern United keeper Liam Little. He parried away a header for another corner and moments later punched the ball clear again.
That desperate defence continued with Southern hustling the ball away following a dangerous goal-mouth scramble in the 17th minute, while defender Danny Ledwith cleared off the line a few minutes later.
Southern’s best chance of the half came in the 30th minute when striker Tennesse Kinghorn turned and drilled a volley that was deflected for a corner.
Auckland’s Micah Lea’alafa put the ball over the crossbar just before halftime and then pushed the ball wide shortly after the break.
Ryan de Vries unleashed a powerful drive as well as Auckland kept mounting the pressure.
Having defended well, Southern launched a counterattack through Conor O’Keeffe. He found Ross Howard, who drilled the ball low and hard but could not defeat the keeper.
The goal, though, came at the other end with Auckland City’s Fabrizio Tavano on hand to toe the ball in.
In the dying moments, Southern pushed forward looking for the equaliser, with even Little leaving the goal. It was a valiant effort but the loss has left Southern United anchored at the bottom of the competition standings with three losses and a draw from four games.
In other games, Canterbury United thrashed the Wellington Phoenix under-20 side 4-1 at English Park. Hawke’s Bay United beat Tasman United 3-1 at Trafalgar Park, while Eastern Suburbs beat Waitakere United 1-0 at William Green Domain.
In the youth league, goals to Ignacio Machuca and Dino Botica saw Auckland secure a 2-0 home victory against Southern United.
