The Phoenix are now up to seventh in the table, two points outside the top six, after preying on the Wanderers' weaknesses at Bankwest Stadium.
Wellington targeted its host at set-piece situations throughout, with Dylan McGowan failing to effectively deal with Steven Taylor, ever a nuisance on the goalkeeper's toes.
Daniel Margush was impeded after 24 minutes as Graham Dorrans headed against his own crossbar from a corner and David Ball touched in the rebound.
The Wanderers were level just four minutes later, though, when Keanu Baccus' shot from the edge of the area escaped the clutches of Oliver Sail.
That goal was awarded despite the offside McGowan hopping out of the way of the attempt, but the home captain was soon obstructing team-mate Margush as Tomer Hemed powered in a close-range header.
That was the 10th headed goal Western Sydney have conceded this season, and coach Carl Robinson complained at half-time: "I can't head the ball for them."
He would have been dismayed to see the Phoenix win three corners within three minutes of the restart, but the Wanderers dug in.
They responded, too, with a 19-shot second-half onslaught, only for Sail and his back line to just about hold out and protect a precious away win.