Queenstown made an intimidating start by scoring in the first minute through Jan Kumar, but local coach Richard Kerr-Bell's side did not panic and equalised four minutes later through big Matt Brazier.
The match continued with Queenstown playing controlled attractive football, despite being short of players and having to include a 16-year-old in its squad. The home side was also depleted when its experienced Brazilian, Henrique Vianna, could not play in the second half.
Green Island took the lead when Max Johnston scored the first of his hat-trick by calmly converting a penalty to make the score 2-1 at the break.
Daniel De Souza started the second half with a blistering drive the Island keeper Stuart Catto did well to save.
But minutes later a jinking run along the bye line past several attempted tackles allowed Johny Quirk to set up Kumar to score again, making it 2-2.
The home side's counter-attacking pace earned another couple of goals in minutes 65 and 69 to give it a healthy 4-2 lead, but Queenstown's pressure really tested the Island defence and a penalty was conceded.
Keeper Catto made a superb save to deny coach Jamie Whitmarsh's side, but continuing pressure breached the Island defence when Sam Harrison scored two goals in the 80th and 85th minutes, and Queenstown chased the winner.
But the fat lady had not finished singing and young Johnston showed a real striker's instinct to pounce on a defensive mistake, outstrip recovering Queenstowners and calmly complete his hat-trick with a 92nd minute winner.
Another in-form young striker was Tennessee Kinghorn, who scored twice with booming shots in Roslyn-Wakari's 2-1 win over University at Logan Park.
Ben Horton scored for Varsity.
Elsewhere, Southland United beat Mosgiel 2-1 despite the home side taking a 12th minute lead through Riley Anderton.
Coach Luis Paiva's side equalised with an untidy far post goal in the 21st minute by George Edwards.
A straight red card to Ryo Okuyama reduced Southland to 10 men, and Mosgiel continued to make chances, but Jack Boland hit the crucial winner with 15 minutes left to give Southland the win, 2-1.
An Andrew Ridden goal preserved Caversham's unbeaten record as his side beat Dunedin Technical 1-0 at Tonga Park.
Northern had the bye.
