Dunedin won a forgettable game when fullback Josh Hamilton kicked two penalty goals in the second spell at Kettle Park.
The standard of play from both sides was poor, with too many handling errors and basic mistakes turning the game into a stop-start affair.
Dunedin had a monopoly of ball and should have won comfortably, but its backline lacked skill and vision and failed to exploit its monopoly of possession.
Green Island made better use of the small amount of ball it received and took a half-time lead of 17-12 when wing Chris O'Neil broke through several weak tackles to score just before the break.
Dunedin dominated in the forwards, with flanker Jon Crossan having a strong game at the break-down.
He also looked dangerous with the ball.
The Dunedin scrum was completely dominant and gained four tightheads.
It monopolised possession and controlled territory in the second spell.
But the backline jitters resulted in the ball being dropped 13 times in the second spell which stymied Dunedin's attempts to turn its forward dominance into points.
Green Island played more attacking rugby and scored two good tries, with fullback Jeremy Cave looking dangerous each time he joined the backline.
Dunedin 18 (Josh Hamilton, Tumua Ioane tries; Hamilton conversion, 2 penalty goals), Green Island 17 (Jeremy Cave, Chris O'Neil tries; Shannon Young 2 conversions, penalty goal).
Half-time: Green Island 17-12.
Referee: Doug Rodgers.
