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The Nix had gone nine games unbeaten under new coach Mark Rudan.
Controversy hit early and late in the clash with the Sky Blues seemingly denied a clear-cut penalty in the first stanza.
In the eighth minute of the game at Westpac Stadium, Wellington's Michal Kopczynski dived for a header in defence, with the ball falling into the path of teammate Louis Fenton.
As he attempted to control the ball, Fenton saw the ball clatter off his arm inside his defensive 18-yard box.
While the handball was not immediately called, it appeared certain Fenton would be penalised following a VAR referral. In bizarre scenes, there was no functioning VAR screen on halfway, so referee Daniel Elder checked the decision on the big screen.
But Elder stood by his original decision, believing there was no clear handball.
Sydney took the lead in the 25th minute.
Siem de Jong tapped home but got injured in Andrew Durante's challenge as he scored.
The Sky Blues suffered another injury blow later in the half, with Anthony Caceres also coming from the field.
Wellington nearly snatched an equaliser late in the game.
In the 82nd minute, Steven Taylor caught Michael Zullo high inside the 18-yard box but instead flung himself forward, seemingly in a bid to earn a penalty.
It worked, with Elder pointing to the spot and the decision upheld after a VAR review.
After some initial difficult with the ball blowing away from the penalty spot, Roy Krishna took the spot-kick.
The poor attempt was comfortably saved by keeper Andrew Redmayne.