A large crowd assembled for the penalty shoot-out, as players - some being treated for cramp - gathered nervously in the centre circle.
Referee Callum Alexander watched closely as penalty takers drove the ball goalwards.
The first to fail was Seamus Gray as Varsity keeper Josh Bell beat away the youngster's attempt.
However, Varsity player-coach James Vaughan then aped David Beckham and John Terry with a skied kick that scattered seagulls as the ball headed towards Opoho.
After five kicks each it was sudden death, and Northern keeper Ike Malpas kept his eye on the ball to make a fine save and win the cup tie, despite gloom broken only by street lamps and passing traffic headlights.
Victory by penalty kicks is dramatic but can be quite unjust.
Both Gray for Northern and Varsity's Vaughan will have nightmares remembering their penalty misses yet both were among their side's best players in fluid play.
There were some good individual performances from Varsity, but the side lost some impetus when key defender Liam Mackinlay went off injured in the first half.
Glad to get a result, Northern coach Steve Brooks was still unhappy with his team's erratic play.
The small Gardens pitch became even tinier as both teams played tight error ridden football on a third of the surface.
At the Caledonian Ground, Dunedin Technical used every square metre to beat Timaru's Northern Hearts 8-0.
Hearts went a goal down after 4min as Ross Mackenzie combined on the left with Tristan Prattley and the young fullback drove forward before lacing a strong shot past Fred Morgan in goal.
Keeper Morgan pulled off some brave saves, and challenged well for crosses, but his defence was regularly pulled out of position.
Another run from deep by another youngster Sam Jasper and Morgan was retrieving the ball from his net again, and when Aaron Burgess made it 3-0 after 20min, the match as a contest was over.
Caversham produced an identical 8-0 score over the Invercargill side Old Boys at Tonga Park.
Carson Gorecki hit a hat trick, Tim Cook got two goals and there was one apiece for Patrick Fleming, Croydon Wheeler and Mike Smith.
Coach Steve Fleming tried several youngsters out in the game's latter stages, and one to have made his presence felt in recent matches is Seamus Ryder.
At Ocean Grove, a defiant Grants Braes scored first when Quinton Gibbons carved through at speed before beating Roslyn-Wakari keeper Peter Evans.
But to celebrate his birthday, man of the match Tom Connor equalised with style and, in the second half, two goals by Ben Keat steered Roslyn through to the next round.
This year's Chatham Cup is required to produce a local finalist, so there is every chance that Dunedin fans will be treated to a top match at either Carisbrook or the Caledonian Ground.
