The win means the Dunedin school has made it through to the top four of the national First XV competition for the first time since 2002.
The newly crowned South Island champion will travel to Rotorua to play Napier Boys' in a semifinal in two weeks.
That prospect seemed unlikely after the opening half at Christchurch Boys' home ground on Saturday. Otago Boys' trailed 12-0 but dominated the second spell, scoring 22 unanswered points before the home side scored a consolation try in the dying moments of the match through centre Michael Green.
Otago Boys' coach Ryan Martin insists he did not say anything out of the ordinary at halftime.
"We just needed to go back to what we do best, which is holding on to the ball and getting quick ruck ball," Martin said.
"Once we started doing that, they didn't know what had hit them and we got a huge roll on."
Otago Boys landed an early penalty to close the gap to 12-3 and, moments later, hooker Sekonaia Pole ripped the ball away in a tackle and ran 30m to score a wonderful try which lifted the visiting team's spirit.
Otago Boys' was dominating possession and strung together "10-12 phases". They used width to stretch the defence and eventually talented lock Josh Dickson scored in the corner.
The third try was in the same mould but this time winger Josh Casey had the honour of crossing the line.
"We were just so dominant in the rucks and mauls and our lineout was superb. I don't think we lost any lineout ball the whole game and we stole a couple of theirs," Martin said.
"And our defence at times was brutal. We weathered the storm in the first half and turned around with plenty of confidence in the second half. There was no panicking or anything. That is the way we have played all year, really.
"It is just a fantastic result and huge for the school."
Christchurch Boys' had opened the scoring when second five-eighth Anton Lienert-Brown sliced through a gap and ran 40m to dot down.
He scored again, from a scrum move, later in the half, barging his way over from about 5m out.
First XV
The scores
Otago Boys' 22
Sekonaia Pole, Josh Dickson, Josh Casey tries: Sio Tomkinson 2 con, pen
Christchurch Boys' 17
Anton Lienert-Brown 2, Michael Green tries: Fletcher Smith con
Halftime: Christchurch Boys' 12-0.
