Former Phoenix striker Tomed Hemed got the crucial goal in the 66th minute, after poor defending from a free kick.
The Wanderers had barely had a chance up until that point, but managed their lead well, before Johnny Koutroumbis scored in injury time, from a swift counter attack after a Phoenix corner, with goalkeeper Oli Sail stranded in the other penalty area.
It brings the club record 13-match unbeaten run, which dated back to April, to an anti-climactic end.
On the balance of play Wellington deserved at least a point, but they couldn't make the most of plenty of pressure, unable to fashion the right final ball often enough, despite plenty of intricate football.
They also failed to get playmaker Reno Piscopo in space in dangerous areas and Gary Hooper was well contained. Midfielder Ben Old, with his first start, had his best performance yet and Tim Payne marshalled the defence well.
But the Phoenix still look vulnerable to set pieces, and so it proved again.
The first half was a tight, physical affair. The Phoenix looked good in possession but struggled to find space in a congested final third, and when they did they were often fouled by the robust Wanderers side.
Fullback Thomas Aquilina was particularly combative, with strong challenges on James McGarry and Piscopo, as Piscopo came in for some heavy treatment through the half.
The Phoenix thought they had gone ahead in the 32nd minute, as Josh Laws poked home a rebound from a corner, but the goal was scratched for offside.
The Wanderers were limited to a Terry Antonis shot from distance, though Payne had to be alert to clear a dangerous Hemed cross.
Wellington's best move came on the stroke of halftime, after McGarry and Ball combined well to set up Piscopo, who directed his half volley straight at goalkeeper Tomas Mejias. The Australian went close again a minute later, slashing a left foot effort just the wrong side of the post.
The Phoenix lifted a gear after halftime, with several half chances. McGarry brought the ball beautifully in the area, but couldn't find the cross, while Wanderers defender Rhys Williams nicked the ball off Hooper's toes, as the English import bore down on goal.
McGarry went close again on the hour, with a thumping half volley from the edge of the area, as the Phoenix had all the momentum.
But completely out of the blue, the Wanderers took the lead, though Hemed, after the Phoenix failed to deal with a free kick.
Goalkeeper Sail made a mess of it, and the Israeli pounced at the far post. The referee didn't give the goal immediately, ruling that McGarry had cleared the ball before it crossed the line, but VAR eventually confirmed it had, which was the correct call.
The Wanderers managed things well from there, slowing the game down and keeping the Phoenix at arm's length. Wellington couldn't find any kind of final flourish, before being undone by the bizarre second goal.
Sail had advanced for a Phoenix corner with two minutes of added time remaining, but was caught out when the Wanderers broke, with Koutroumbis completing the easiest finish of his career to date.
Western Sydney Wanderers 2 (Tomer Hemed 66, Johnny Koutroumbis 92)
Wellington Phoenix 0
Halftime: 0-0
