Waitaki led 12-5 in the 55th minute of the Otago premier schools game and looked likely to hold on to score an upset win on its home ground.
A missed penalty goal by the men in black - who scored a converted try early in the second half after scores were locked 5-5 at halftime - with about 16 minutes to go proved something of a turning point, seemingly sparking McGlashan.
The Dunedin school showed plenty of class in the final quarter, though the eventual winning margin flattered it.
In a match played in frigid conditions - the air temperature was 5degC but the wind chill factor meant it was much colder than that - both sides were guilty of too many handling errors and other inaccuracies.
McGlashan had looked frustrated for much of the game but its replacement players visibly lifted the side, and coach John Kyle paid tribute to his bench after the game.
''I thought we showed great character at the end,'' Kyle said.
''We got massive value off the bench. Every one of our guys who came on delivered energy and brought momentum.''
Waitaki was well served by its physical forward pack, especially hard hitting No 8 Sailosi Vea and openside flanker Josh Hayward, while prop Arthur Burdon, flanker Rory Ferguson, Reece Stackhouse and the bench players were best for McGlashan.
In the other top six games, South Otago High School beat the Otago Boys' High School Second XV 21-18, and King's High School beat Dunstan High School 48-21.
