A first half Paul Ifill penalty separated the sides, preventing Gold Coast from joining Melbourne Victory on top of the table and pushing the Phoenix into the top four.
Wellington begun brightly and were pressuring Gold Coast with their forward forays and were quite unlucky not to go a goal up when Adrian Caceres swung a free-kick into the path of his captain Andrew Durante who was unable to knock it in from close range.
Gold Coast keeper Jess Vanstrattan was beaten but the upright saved the day for the home side.
Gold Coast were able to wrestle back some ascendency and had plenty more of the play after their earlier scare but the Phoenix defence held strong with their opposing strikers having to deal with plenty of off-side calls.
On the brink of half-time, the Phoenix were awarded a penalty when Gold Coast defender Bas van den Brink challenged Tim Brown on the edge of the area but referee Matthew Breeze deemed the tackle to be too strong and pointed to the spot.
Paul Ifill stepped up to the plate and duly converted with a well-taken spot-kick to give his side the lead going into the break.
Both sides rang the changes at the beginning of the second half as the rain came down on the Skilled Park fans but Gold Coast couldn’t get themselves back into the match and fell for a second time to Wellington this season.
The loss pushes Gold Coast down to third as Wellington jumps into fourth a week out before their first finals appearance.