The Phoenix got off to an awful start when left back Tom Doyle scored a calamitous own goal in the 12th minute following a miscommunication with goalkeeper Glen Moss.
It's been a tough start to life as an A-League player for Doyle who also contributed to one of Perth's goals during Wellington's season-opening 2-1 loss to the Glory last Sunday.
To Doyle's credit he didn't appear to let the error visibly drag him down as he slowly worked his way in to the game.
Finding a reliable left back was one of Merrick's biggest problems last year and Doyle impressed during the pre-season so he will likely hold on to the position in the short term.
After they gave away the lead, Wellington fell out of the contest as they went flat. The Mariners enjoyed lengthy spells of possession, while the visitors were barely holding on.
That changed when out of nowhere Jeremy Brockie made a nice run in to the box and was brought down as the Phoenix were awarded a penalty.
Brockie, who has a mixed history with spot kicks, stepped up to the mark. His penalty rattled in to the crossbar but luckily Michael McGlinchey was on hand to head home as Wellington drew level.
McGlinchey's goal also glossed over the fact that Brockie's penalty missed the target and it's an area that needs to be addressed by Merrick, particularly following the departure of the accurate Carlos Hernandez.
Penalties are not something that sides can rely on but when they're awarded you must have a player in your ranks who can confidently take them and convert them.
The goal gave the Phoenix a much-needed boost as they began to believe they could compete with the Mariners who appeared to be running on fumes given they also had a mid-week FFA Cup fixture to contend with.
Wellington's movement proved challenging for the Mariners to maintain as the Phoenix's front three of Brockie, McGlinchey and Nathan Burns caused havoc up top.
That pressure eventually told when Brockie nodded back a Doyle cross to Burns who gave the Phoenix the lead in the 53rd minute.
It was a deserved goal for Burns who missed a one-on-one during last week's defeat to Perth.
The final 15 minutes were frenetic as the Mariners hit the post as they poured players forward, while Moss was also called in to action regularly.
But to Wellington's credit, they held on and banked a valuable three points.
Wellington Phoenix 2 (Michael McGlinchey 35, Nathan Burns 53) Central Coast Mariners 1 (Tom Doyle 12 own goal) halftime: 1-1
