With expectactions high pre-game Wellington have paid the price for a slow start as Western Sydney laid down a significant marker in the race for the last finals spot.
Gui Finkler's sublime freekick made for a tighter finish but Phoenix left themselves too much to do after an uncharacteristically poor start.
It was a strangely subdued opening from Phoenix who ceded early possession to their hosts, and it was Jumpei Kusukami who fired an early warning shot - striking Glen Moss' lefthand post.
Wanderers didn't have to wait too long to go one better as Nico Martinez collected a loose ball and slotted home in the 9th minute from around the eighteen-yard-box.
It drew the ire of captain Andrew Durante who raced to confront the referee with replays suggesting a possible Wanderers foul in the build up.
The decision sparked a response from Wellington who began to enjoy some good spells of possession, with Finkler and Kosta Barbarouses combining well to carve out the visitors' first half-chance of the game but the Wanderers defence scrambled well to avert the danger.
Adam Parkhouse made way after half an hour and Tom Doyle came on, and was immediately into the action putting in a robust tackle on Scott Neville.
Finkler then had Vedran Janjetovic scrambling in the Wanderers goal, but his viciously struck freekick flew wide of the post.
With Phoenix very much on top it was a sucker punch from Wanderers as Brendan Santalab continued his hot form against the Nix striking a second goal for the hosts in the 38th minute.
Even yet Wellington could have halved the deficit in the shadow of half-time but for an excellent save from Janjetovic, denying Barbarouses from distance.
Roly Bonevacia entered the fray at the change but he had little chance to make an impact before Phoenix found themselves further in arrears as that man Santalab stooped to head home a morale-sapping third.
Topscorer Krishna continued to toil and he drew a foul out of Jack Clisby in a dangerous area. At the second time of offering Nix's set-piece maestro Finkler showed his quality, drilling it home past a hapless Janjetovic.
In the 87th minute the Brazilian had the chance to repeat the medicine, setting up some nervy moments for fans in red and black as a comeback threatened, but a nine-man wall did its job blocking Finkler's effort.
Phoenix probed, looking for a second goal, but the Wanderers defence stood firm, garnering themselves an important three points.