Basing its game around a solid set piece, South Otago led 16-6 at the break and clinched the game with quarter of an hour left, when right winger James Pike toed ahead a loose ball from 40m out to score right beside the posts.
South Otago coach Dave Latta was thrilled with the win, especially after the side had come up just short last year, going down 9-6.
It could have won by more but a try to left winger Lachie Moore was ruled out in the dying minutes for a marginal forward pass.
Latta paid tribute to the strong scrum fielded by South Otago which, time after time, disrupted the Central Otago front eight.
The forwards also pilfered plenty of ball at line-out time and dominated at the breakdown.
Latta said the side had trained hard and had come together well.
"We applied what we wanted to do on the field today. It was just good old country rugby. Guys really getting into it and giving it their all," he said.
Central Otago coach Richie Anderson said South Otago fully deserved its win, and his side was too slow to start.
He felt his team came back into the match in the second 20 minutes of the game but Pike's try, which came after the ball was lost in the Central midfield, was the backbreaker. Both sides were willing and there was plenty of vigour in the tackling.
Often, there was space on the outsides but players preferred to hit the ball up.
Central Otago first five-eighth Reece Winter opened the scoring for Central Otago with a penalty after two minutes but Sam Young quickly replied for South Otago.
South Otago centre Blake Korteweg then scored the first try of the game following a couple of attacks near the line, after 12 minutes.
The ball came to the Clutha centre 10m out, and he shrugged off the tackle of Central Otago halfback Simon Williams to score.
Central Otago came back into the match after 15 minutes of the second half when Winter made a nice dab and fed fullback Ben Purvis who dived over in the corner.
But South Otago swung back on to attack and Pike's score clinched the match.
Best for the Central Otago team was Winter while No 8 Ben Blakely made a couple of good breaks.
In other games, Central development beat Southern 14-12, Central under-18 beat Southern under-18 17-0, Southern under-16 beat Central under-16 27-15 and Southern under-14 beat Central under-14 37-10.
Topp Cup:
South Otago 26 (Blake Korteweg, James Pike tries, Sam Young four penalty goals, two conversions) Central Otago 11 (Ben Purvis try, Reece Winter 2 penalty goals).
Half-time: 16-6.
Crowd: about 700.
Players to impress in Milton
Matt Faddes: The South Otago schoolboy ran well from fullback, gliding through gaps and was sound under the high ball.
Sam Young: Made a couple of good breaks and kicked well.
Dave Kenney: The halfback contributed plenty to the win, running well and finding his outsides, though his day was clouded when he left the field with a troublesome shoulder injury.
