Hernandez has also been the subject of recent speculation surrounding how happy he is at the club as he waits on his family to arrive from Costa Rica, but those concerns didn't appear to be a factor as he suited up today.
Phoenix coach Ernie Merrick also made a tough call by dropping the out-of-form Jeremy Brockie for the veteran Ifill after the latter had displayed good energy from the bench in recent weeks.
Sydney were nearly gifted the lead inside the first 10 minutes but Joel Chianese couldn't finish with an open goal at his mercy.
After enjoying a collection of decent chances during the first half an hour, the Phoenix finally broke the shackles via Stein Huysegems in the 33rd minute.
The former Belgian international had spurned a couple of earlier opportunities but didn't need any further invitations as he linked nicely with Hernandez to round Sydney goalkeeper Vedran Janjetovic to collect his third goal of the season.
Huysegems made a beeline to the Phoenix bench to celebrate as they welcomed him with open arms.
The goal was due reward for Wellington who had the better of the first spell and defended well during a nervous final few minutes to take their 1-0 lead to the break.
The home side were then dealt a major blow only minutes in to the second spell when Ifill was taken from the field on a stretcher with a suspected Achilles tendon injury.
The former Barbados international hit the deck with nobody impeding him and immediately signalled to the bench in agony, which brought Brockie in to the fold.
Sydney enjoyed a nice patch of possession to begin the second half and the Phoenix were forced to take cover and defend, which they did strongly with captain Andrew Durante leading the charge.
Hernandez had the opportunity to ice the game when he combined with Huysegems again in the 65th minute but his shot was saved by Janjetovic.
Wellington were able to shut down Sydney for much of the game as the visitors regularly tried to play the ball out from the back but lacked fluency with their passing.
They were without marquee man Alessandro Del Piero who missed the game with back and hamstring niggles, while Brett Emerton was also sidelined.
In the end it was Wellington's night as Merrick was given his first win as Phoenix coach.
Wellington Phoenix 1 (Stein Huysegems 33) Sydney FC 0 Halftime: 1-0