© Getty Images
The home side spurned the chance to take the lead inside the first 10 minutes when Roly Bonevacia missed from the penalty spot.
Phoenix were made to pay for the miss four minutes later when Ibini put Sydney ahead with a powerful finish.
Ibini nearly claimed a second two minutes later with a header, but the effort was well saved by Phoenix keeper Lewis Italiano.
The Sky Blues were awarded a spot kick just after the half-hour mark when Kiki Naumoff was fouled inside the area.
Smeltz took the resulting penalty to give the visitors a two-goal advantage, before Milos Dimitrijevic went close with a free kick just before the break.
Two minutes into the second period, Boxall reduced Wellington's deficit with a smart finish from a short corner that caught the away side off guard.
However, Sydney were able to withstand second-half pressure from Wellington to secure second place in the division.