Victory was more or less secured in the final half of the first spell when South Otago posted three tries to lead 25-5 at the break.
Waitaki Boys' responded with a strong second half, outscoring its opponent 26-20, but coach Wayne Kinzett said his side struggled to contain South Otago's midfield.
''They busted us a lot in the midfield,'' he said.
''But once we got that sorted, we scored some good tries. It was just too little, too late, really.''
Waitaki Boys' played Southland Boys' High School on Wednesday and Kinzett wondered what impact that had had on his team.
''We knew it was coming, so it is no excuse. We've got a wee bit of work to do but we showed glimpses of what we can do.''
South Otago coach Adam Whaanga had the opposite experience. His side started strongly but faded after he made several key changes in the second half.
''Waitaki Boys' had been travelling nicely, so we knew it was a big game for us,'' Whaanga said.
''We were pleased with how it all went. But, to be fair, we made a few changes and we actually struggled to stop them in the end. We thought we had a bit of a buffer and just about made a wee bit of a blue.''
Waitaki Boys' flanker Salesi Vea scored twice and hooker Kafa Katoa also had a strong game.
No 8 Sam Fischli was a standout performer for South Otago. He was dynamic in the loose, tackled hard and broke the line. Fullback Rory van Vugt was on hand to score a couple of tries through wonderful positional play.
In other games, Dunstan High School beat St Kevin's College 52-38, King's High School beat Mt Aspiring College 53-17, John McGlashan College beat Kavanagh College 67-5, and the Otago Boys' High School Second XV beat winless Taieri College 69-6.
