Southern put in a strong performance against the wind, and took a 28th-minute lead through Andrew Ridden, who drove in a right-wing corner delivered by Cody Brook.
The first half produced controlled football from Southern which absorbed some decent attacks by Wanderers and mounted a mixture of short passing attacks and breakaways by Lewis Jackson and Jeremy Fong.
Wanderers impressed local supporters, with the added ingredient that three Football South players - Ben O'Farrell, Oliver Ceci and Ben Kiore - were playing for New Zealand under-17 coach Jose Figueira, whose target is a place in the Fifa youth tournament in Chile in 2015.
Southern spurned a couple of good chances in front of goal, and later paid a heavy price, as Wanderers appeared transformed in the second half.
Coach Figueira then tightened his defence by pulling back Billy Jones just in front of centrebacks Ban Mata and Luke Johnson, and from that platform, Wanderers gained more control.
Kiore did his eventual chances of travelling to Chile no harm at all, when he was first to a loose ball in Southern's goalmouth after keeper Josh Dijkstra blocked a shot, and Kiore rammed in his fourth goal of the season in the 52nd minute.
Tails up, the Wanderers poured forward, and Southern's defence allowed space for Jack Anderson and Kiore to test Dijkstra.
Yet with Ridden powerfully winning ball possession in midfield, and Rahan Ali, Riley Anderton and Cody Brook still feeding and supporting striker Jackson, there were enough near misses to keep spectators roaring encouragement as both teams chased the next goal.
It was referee Calvin Berg who stepped into centre stage, spotting a hand ball in the Southern penalty area and pointing to the penalty spot in the 74th minute. Wanderers captain Mata expertly drove the spot kick past Dijkstra's despairing dive.
Coach Kevin Scoullar pushed centreback Tyrrell Barringer-Tahiri forward but Southern made no further headway, and conceded a third goal in the 90th minute.
''Our second-half performance was poor,'' Scoullar said.
''Overall, we had our chances to win, but they stuck to their game plan, and deserved the win.''
In the women's national league game played in Cambridge yesterday, Football South was thumped 7-1 by Waikato-Bay of Plenty, with Alex McIntosh getting South's consolation goal.
