The visitors got off to the best possible start, stunning the home crowd when Henrique Alves-Viana chipped Danny Robinson in the third minute.
Tim Myers snuck home a scrappy equaliser in the 39th minute and normal service seemed to have resumed. But Southern went back in front three minutes later, with Peter Rae taking advantage of a defensive mix-up.
When Morgan Day received his second yellow card the stage seemed set for Waitakere to snatch a come-from-behind victory. That idea lasted for only three minutes, though, as Logan Wright-Webb tucked home from a goalmouth scramble.
Waitakere piled forward in an attempt to pull themselves back into the game, but Southern held on.
Auckland City made the most of the rivals' mishap and went one point clear with two games in hand after a 3-2 win over Team Wellington at Kiwitea St. Two Emiliano Tade goals sandwiched a Ryan de Vries strike to grab all three points, with two late goals from Wellington providing a nervous finish.
Elsewhere, Canterbury United and Hawkes Bay United drew level with Waitakere to create a congested top half of the table. Canterbury edged WaiBOP United 1-0 at home, while Hawkes Bay beat Wanderers at North Harbour Stadium.