The incredible win moves Phoenix into third place, just a point behind leaders Melbourne Victory and SydneyFC.
Wellington was searching for a first win in four matches to keep alive its hopes of a Premiers' Plate and cement its place in the top four.
While Phoenix had a few early half chances, it was Central Coast that hit the font on 11 minutes.
Isaka Cernak played Nick Fitzgerald though into the area after he timed his run to perfection. Fitzgerald kept his cool with only Glen Moss to beat and side-footed home to give the Mariners a 1-0 lead.
Wellington continued to have the better of play but failed to deliver the final pass in the opposition box or was thwarted by desperate Central Coast defending.
On 36 minutes the home side was hit with another sucker punch. Free-kick specialist Eddy Bosnar lined one up from outside the area and drove his shot into the bottom corner to double the Mariners' advantage.
Wellington's best moment of the first half came just before the interval as Roy Krishna cut inside from the left and forced Liam Reddy into a difficult save.
From the resulting corner Phoenix hit the bar with a header before Central Coast scrambled clear.
Wellington came out for the second with great determination to drag itself back into the contest.
After more missed opportunities Roly Bonevacia pulled one back for the host's as he rifled a shot from the edge of the penalty area beyond Liam Reddy and into the far bottom corner to make it 2-1.
Phoenix continued to pile on the pressure and it finally paid off with just over 10 minutes remaining. Bonevacia was dispossessed on the edge of the area, but the ball fell perfectly into the path of Kenny Cunningham in the box and he slotted in to draw the host level.
Wellington pushed forward in desperation as the clock ticked down and with just seconds left the ball once more fell perfectly in the path of Cunningham who expertly dispatched it into the bottom corner to complete the turn around for the host.
While coach Ernie Merrick was happy with the fight his team showed, he thinks its tendency to concede early soft goals is a worry.
"There were two cheap goals, one within 10 minutes again," he said.
"You can't play like this going into finals - we may as well give it away now if we're not going to get into goal-scoring positions."
"It was just good to see the boys stepping up to prove to themselves that they really go at teams confidently," he said.
Newly-signed Mariners coach Tony Walmsley believes his team was punished as it struggled to contain the Phoenix midfield in the second spell.
"With and without the ball in the second half, we had problems, and that's the work in progress," Walmsley said.
"At no time did we want to be sitting as deep as we were... we're trying to play a proactive, higher line and press earlier but they worked very well in the midfield to get numerical superiority around the ball."
