Southern won the game in the first half when it dominated possession and led 5-3 playing into a 20-point gale at Kettle Park.
The Southern forwards gained 85% of the ball and it was kept tight in the forwards for the first spell.
The inside pairing of Lewis Hancock and Julius Glasson controlled the ball and fed it back into the forwards.
Dunedin was not able to get hold of the ball.
The only try of the spell came from a mistake by Southern fullback Hamish Buick when his clearing kick went up in the air.
But fortune favoured Southern because the ball bounced awkwardly and eluded the Dunedin defenders and ended in the arms of Southern winger Nik Tupaea, who sprinted 40m for the try.
Dunedin monopolised possession when it played into the wind in the second spell and took the lead, 8-5, when prop Keith Cameron scored after a rolling maul.
Two penalty goals by Glasson took Southern back into the lead 11-8 and it added two tries in the last 10 minutes.
The first came from skilled play by Glasson, who sent a wide pass for winger Greg Zampach to score wide out, and fullback Hamish Buick scored in the last minute after Dunedin turned over ball 40m out.
Southern was a solid unit in the forwards with loose forwards Sam Crompton and Carl Anderson and lock Uili Kolo'ofai playing impressively.
The best Dunedin players were Will Henry and Kelsey Miller in the front row and Robbie Smith at halfback.
Southern 21 (Nik Tupaea, Greg Zampach, Hamish Buick tries; Julius Glasson 2 penalty goals), Dunedin 8 (Keith Cameron try; Robbie Smith penalty goal).
Halftime: Southern 5-3.
Referee: Doug Rodgers.
