But they will look back on this match as one that got away. They were comfortable at 1-0 — with several chances to double their lead — and will rue the momentary loss of concentration which let the Melbourne team in for their equaliser just before the hour mark.
Hemed worked hard for his two goals, while Tim Payne was outstanding at the back for the Phoenix.
Both teams were missing key men, with Mexican Ulises Davila (hamstring) a big loss for the Phoenix, while Andrew Nabbout (adductor) has been influential for the City. With one eye on the playoffs, City coach Patrick Kisnorbo made six changes to his team, while Steven Taylor (illness) was a late withdrawal for the visitors.
The reshuffled City team struggled for rhythm in the first half, but it was also a product of excellent work from the Phoenix, who were sharp, strong and well-structured.
Reno Piscopo could have opened the scoring in the 33rd minute, after being set up by Louis Fenton. The Phoenix made regular inroads down the right, and from one such raid, the ball was cut back to Piscopo, but the Olyroos midfielder scuffed his shot.
Moments later, Fenton was again in space and won a penalty, after being bundled over by Ben Garuccio. Hemed's spot kick was cool and composed, as he waited for the keeper to commit before rolling the ball into the opposite corner.
David Ball had a chance moments later — after a quick transition — but directed his shot straight at the keeper.
Ben Waine could have extended the lead just after halftime, as he rounded the keeper after collecting a precise long ball, but his shot was cleared off the line brilliantly, while moments later, Hemed miscued after being set up from 10 metres out.
The Phoenix had looked more likely, but after all their hard work, the Melbourne City equaliser in the 58th minute was a gut punch. A heavy touch from Cameron Devlin was followed by Joshua Laws dallying with a clearance, which led to Naoki Tsubaki scrambling home from close range.
Substitute Jaushua Sotirio was denied from three yards by Tom Glover, when it looked easier to score, before Oli Sail made a strong save from Craig Noone.
But a brilliant free kick from Jamie Maclaren — from 25 metres — broke Phoenix hearts. It was a great strike, though the Wellington wall looked slightly misaligned.
They looked headed for an undeserved defeat, before a brilliant piece of improvisation of Hemed.
The Israeli international flung his left foot at a precise David Ball cross, brilliantly directing it goalwards with the outside of his boot to level the scores.
Melbourne City 2 (Naoki Tsubaki 58, Jamie Maclaren 82)
Wellington Phoenix 2 (Tomer Hemed 37 pen, 88)
HT: 1-0