Green Island achieved a major upset when replacement prop Stewart Maguire crashed over in the corner for the winning try in the final seconds at Miller Park.
It was a game Harbour should have won because it had 75% of territory and possession through the efforts of flankers Eben Joubert and Jason Kelly and prop Ben Nolan.
But it made too many mistakes and squandered its hard-won possession with an ill-disciplined display by a backline that passed on too much 50-50 ball and made too many unforced errors.
Green Island was a team that played with passion and was determined to win the game.
Winger James White, the best back in the Harbour side, scored the first try of the game when he took a pass from Nolan and ran 40m.
Fullback Johnny Hughes, who kicked four penalty goals, stretched the lead to 14-6 with a penalty 15 minutes into the second spell.
But the gap was reduced to one point, 14-13, when fullback Jeremy Cave used his speed to score a try for Green Island.
Cave, winger Chris O'Neill and flanker Jason Bint also had strong games for Green Island.
Green Island 18 (Jeremy Cave, Stewart Maguire tries; Tino Elisara conversion, 2 penalty goals), Harbour 17 (James White try; Jonny Hughes 4 penalty goals).
Half-time: Harbour 11-6.
Referee: Todd Pullar.