Nelson's Omar Guardiola grabbed centre stage by setting up an early goal for Josh Lis, then spun wide on the right wing to lace a superb narrow angled shot past Southern keeper Tom Stevens.
The Southern team, coached by Mike McGarry and Andrew Brook, played controlled football with quality passing moves but possibly indulged in an extra pass in front of goal and suffered for that.
Nelson coach Davor Tavic was pleased with his team's performance in difficult conditions and, apart from Guardiola, singled out centre back Fox Slotemaker and youngsters Zac Muir, Sam Wilson, Jamie Creswell and Bertie Fish.
Southern mounted many attacks but failed to finish effectively, despite top matches from James McGarry, Cody Brook and Rahan Ali.
''There were some really good phases of play but we just did not manage to capitalise,'' Mike McGarry said.
