Injuries to key players took their toll on Southern as Dunedin controlled the game in the second spell at Kettle Park.
It was an even game in the first spell, which ended 14-14 when Dunedin halfback Brad Webber scored close in.
Southern had the game in control in the first spell when wings Joe Hill and Harry Uffindell scored tries and it led 14-7, but it lost fire power when centre Nick Jones was injured and failed to win lineout ball when lock Tom Franklin left the field.
Dunedin had the better scrum and controlled the tight exchanges through prop Kelsey Miller and hooker Will Henry.
Dunedin bumbled its way through the first spell and failed to put phases together, but it got its act together in the second spell. It took the lead when it put continuity into its game and replacement loose forward Mark Atkins scored to take it into a 24-19 lead.
There were nine injury replacements and the game lost structure in the last 20 minutes, especially when the scrum was de-powered.
Dunedin loose forwards Gareth Evans and Mitchell Zandstra controlled the game in the second spell.
First five-eighth Ben Patston had a sound kicking game for Southern and hooker Johnny Mason was lively.
Dunedin 27 (Pera Gibbs, Mark Atkins, Brad Webber tries; Liam Edwards 3 con, 2 pen), Southern 19 (Joe Hill 2, Harry Uffindell tries; Ben Patston 2 con). Halftime: 14-14.
Referee: Jeff Grubb.
Dunedin ... 27
Southern ... 19