The game looked assured for the home team in the 78th minute when Ben Sigmund made it 2-0, following acting captain Tim Brown's goal two minutes after the restart.
But Sydney responded from the restart through dangerman Joel Chianese and the switched-off Phoenix paid dearly two minutes later when the 22-year-old striker levelled the scores with eight minutes remaining.
Phoenix go-to man Paul Ifill delighted the 10,019 crowd a minute later, with a well-taken penalty after he was brought down by Sydney defender Michael Beauchamp.
Chances were few and far between early on, both defences locked down tight and no shot was fired in real anger until Brett Emerton delivered a beautifully weighted ball into the area, but Bruno Cazarine blasted his shot well clear.
Sydney gradually started finding some rhythm, but couldn't time the final delivery and the Phoenix's hard-working back four looked comfortable in holding out the Sky Blues.
Wellington gradually worked their way back into the game, lifting in the midfield and running with more urgency in the attacking third, but an uncompromising defensive effort from Sydney held strong.
Referee Chris Beath delivered four yellow cards in the first spell, two to each team, and the halftime whistle sounded on a scoreless draw.
Brown's goal kickstarted the Phoenix two minutes into the second half, and the game exploded into an entertaining end-to-end second-half spectacle.
