The Mariners had endured a terrible start to the season with two draws and nine losses from their previous 11 games, but the Phoenix didn't make it easy for themselves.
They needed three second half goals to get the job done as they toasted club legend Andrew Durante's 300th A-League appearance, the most by any player in competition history.
The opening exchanges didn't go to plan for the Phoenix and they found themselves down 1-0 after only eight minutes.
Mariners forward Matt Simon, now in his third stint with the club, was fouled by Phoenix defender Steven Taylor and then made no mistake from the spot to convert the penalty.
The Mariners won seven corners during the first 13 minutes, which gives you an idea of the pressure they applied to the Phoenix.
That pressure eventually told as Andrew Hoole made a gorgeous run to latch onto a Jacob Melling pass to double the advantage.
Playing without their usual midfield due to the suspensions of Alex Rufer and Mandi, the Phoenix looked lost in the centre of the park. Melling and Matthew Millar were having their own way on the ball as the Mariners enjoyed the run of the race during the opening 30 minutes.
Michal Kopczynski and Mitch Nichols were charged with plugging the gaps in the midfield for the Phoenix and they weren't able to stamp their mark on the contest.
Nichols may have been short of a gallop given he last started an A-League match in round four in November.
It was the substitution of Nichols at halftime for new recruit Cillian Sheridan that sparked the turnaround in fortunes for the home side.
Before all of the crowd had returned to their seats, Roy Krishna was through on goal and was fouled by Kye Rowles in the box.
Rowles was sent off leaving the Mariners with only 10 men and Krishna then scored a penalty of his own.
The Fijian international added another spot kick shortly after as Wellington gained parity on the scoreboard in the 58th minute at 2-2.
Krishna also had a hand in the winner as Phoenix striker David Williams put them ahead with less than half an hour to play.
A healthy crowd of 10,186 was on hand to enjoy an entertaining clash as the Phoenix solidified their spot inside the A-League's top six, and the fans removed their shirts as the clock ticked past 80 minutes as they danced in the stands.
Jordan Murray nearly stole a late leveller for the Mariners but it was ruled out as he was offside.
The playoffs are still a long way in the distance but the Phoenix know they're heading in the right direction under Mark Rudan's coaching.
Wellington Phoenix 3 (Roy Krishna 48 pen, 58 pen, David Williams 65)
Central Coast Mariners 2 (Matt Simon 8 pen, Andrew Hoole 21)
Halftime: 0-2
