The loss, Otago Boys' only one this year, means Christchurch Boys' will represent the South Island in the top four schools competition in Rotorua this weekend.
Despite ''blowing'' a couple of chances to win at the death after staging a late fightback, Otago Boys' coach Ryan Martin was proud of the team.
''We definitely threw everything we had at it, which is great from a coaching perspective. To see your team go out like that, rather than falling by the wayside.
''That game will be great for the team next yea. The boys who are back will remember that. Sometimes a loss is as good as a win in situations like that; you learn a lot about yourself,'' he said.
Otago Boys' trailed 28-13 inside the last 15 minutes, before winger Josh Buchan bagged a double to set up an enthralling finish.
With time running out, Otago Boys flanker Matt Heffernan was tackled short of the line and Christchurch Boys' turned the ball over to avenge their 29-7 loss on the same ground in July.
Otago Boys had started the match well, jumping out to a 10-0 lead with a Heffernan try and Sio Tomkinson penalty.
However, Christchurch Boys' hit back with two converted tries late in the first half to lead 14-10 at the break.
Otago Boys' set piece was not up to its usual high standards on Saturday and Martin conceded pressure got to his team.
''We were just slightly off yesterday. We made a couple of errors at set piece time that we normally don't make, which probably summed up and cost us the game to be honest.
''It's a big occasion and pressure can do funny things. In those type of games it can be just two errors that can cost you, and that's what happened to us.''
Players did not hide their emotions at fulltime, especially the nine year 13s who played their last game for the Dunedin school.
''I haven't seen that much emotion in the changing room. As a coach that's not a bad thing, it's a good thing. Because I think after a game like that players go on and become better players.
''It was a game within our grasp and they will remember that,'' Martin said.
''There's some really good talent in this team and the province is going to have some really good players going through the system.''
Departing midfielder and co-captain Tomkinson played 64 straight games for the first XV, something Martin doubts will be repeated.
Martin will now move into his head coaching role with the New Zealand schools Barbarians side and will travel to Rotorua for the top fours competition this weekend to begin choosing his squad.
However, he will ''definitely'' be back coaching the Otago Boys' first XV next season, which should have 13 players from this year's team.
By Robert van Royen.
South Island final
The scores
Christchurch Boys' 28
Hayden Webber, Fraser Scott, Alex Nankivell, Ethan Simpson tries; Josh McKay 4 con
Otago Boys' 24
Josh Buchan 2 tries, Matt Heffernan try, Sio Tomkinson 1 pen, 3 con.
Halftime: Christchurch Boys 14-10
