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.