While the final score might appear comfortable, the defending champion Saints did not have the game in the bag until Matt Gillan and James Ross killed the students off with a few daggers from beyond the arc in the final three minutes.
Varsity captain Sam King, who led all scorers with 28 points, knocked down his fourth of five three pointers to pull his side to within 74-71 with three minutes 15 seconds left on the clock.
But on the Saints' next possession, Gillan (24 points) did what he does best - strike from deep.
Ross (23 points) made it 80-71 a few moments later with a typically clutch jumper from long range, before Gillan knocked down his sixth three pointer of the match to make it 83-71 with a minute left.
King promptly drained another bomb, but the Saints had finally fended off Varsity's rally.
Varsity did not help its cause with a poor showing from the free throw line in the final quarter, where it missed nine of 13 attempts.
The students were playing catch up for all but the first few seconds of the match, after Emerson Watson (22 points) opened the scoring with a layup on the game's opening possession.
A huge first quarter, in which the Saints connected on five of nine shots from three point land, propelled St Kilda to a 30-14 lead after 10 minutes.
However, Varsity came storming back with a 24-8 run, which was highlighted by a booming alley oop dunk by Sam Colenutt to knot the game up at 38-38.
The Saints finally called a time out with 2min 19sec left in the half to regroup, and Saints guard Tom Ingham (10 points) immediately hit a jumper after the break to help his team take a 47-43 lead at the half.
Watson pulled Varsity to within 54-51 early in the third quarter with a pair of three pointers and a floater, but his side then went cold from the field for five minutes.
King, who was briefly sidelined after rolling his left ankle late in the second quarter, finally ended the rut with a layup inside the last minute of the half, but the Saints took a 63-56 lead into the final quarter, and ultimately saw off the students.
In the day's other games, Falcons A (7-3), which has two deferred games up its sleeve, beat the Bombers (5-7) 82-66, while Micah Lepaio drilled six three pointers in his 26 point haul to help Magic A (6-5) thump Varsity B (0-11) 94-51.
Otago's boys and girls under 17 teams finished ninth and 10th respectively at the national under 17 championships in Auckland on Saturday.
The boys beat Southland 89-75 in their ninth and 10th playoff, while Southland reversed the result in the girls section, winning 62-48.
