Second-half goals to Eliza Familton and Isabel Gomez lifted the defending champions to fifth on the ladder and prevented the Phoenix from making any ground on leaders Melbourne City.
Second-placed Phoenix would have got to within three points of City had they won, but Wednesday's loss leaves them six points adrift with two games left.
They are only one point ahead of Canberra and Adelaide.
Phoenix, who have lost all six games they've played against the Mariners, had nine more shots but only one more on target than the hosts.
Teenager Familton marked her first ALW start with just her second goal, heading in a Peta Trimis cross in the 58th minute.
Midfield dynamo Gomez, who had two previous shots saved by Victoria Esson, blasted an unstoppable 83rd-minute effort in from the edge of the penalty area.
Former Mariner Brooke Nunn hit the crossbar with a fierce shot in the 54th minute, but the Phoenix had to wait until the third minute of added time for their goal.
Macey Fraser brilliantly converted a long-range free kick lifting it over the wall and past the goalkeeper.
It was the Mariners' first win in four home matches and Wellington's first loss in their last seven away games.
"Credit to Central Coast, they made our lives difficult and they scored two great goals," Esson told Ten and Paramount Plus.
"In regards to the title playoff we've just got to take it week by week."
Both teams struggled to test the goalkeepers in the first half, but created better chances after the break.
"The girls really needed the win tonight to progress to the finals. It feels amazing to get the win, we've been working so hard," Familton said.
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