Utility loose forward Isaac Milne crashed over for the winning try in the last act of the game when Southland Boys' High School was beaten 23-20.
It was the first time Waitaki Boys' had beaten Southland Boys' in Invercargill for more than 20 years.
Waitaki Boys' led 13-7 at the break but Southland Boys' came back strongly to lead 20-16 midway through the second spell.
It was a desperate last five minutes, with Waitaki Boys' camped inside the Southland 22m. The wining try came after Waitaki had won five rucks.
The stand-out players for Waitaki were lock Don Lolo, who also scored a try, fullback Jamie Robb, and second five-eighth Levi Fogarty.
Waitaki Boys' will play Otago Boys' in the last top-four round robin game this Saturday.
The teams will meet again in the final.
Otago Boys' scored eight tries when it beat King's High School 50-0 in the other top four game.
Otago Boys' led 31-0 at the break and added 19 more points when playing into the strong head wind in the second spell.
Halfback Josh Renton directed play efficiently and lock Brendan Murdoch had his best game of the season.
Hooker Sekonaia Pole was a rugged defender.
St Kevin's College had a comfortable 26-7 win against Gore in Oamaru to give itself a chance of making the final of the middle-four competition.
St Kevin's scored four tries to get the vital bonus point.
The tries were scored by halfback Facunado Briones, centre Gaston Bazan, No 8 Ash Miller and midfield back Tim O'Malley, who also kicked three conversions.
Dunstan booked a spot in the middle-four final when it beat South Otago 17-7 in Balclutha.
Midfield back Sam Galletly, first five-eighth Callum Clark and winger Daniel McBreen scored the tries.
A feature was the strong Dunstan defence that restricted South Otago to one try in the second spell.
In the bottom four games, John McGlashan College beat James Hargest High School 31-18, and Menzies College beat Kavanagh College 47-10.
