The hosts got off to a promising start having had the lion's share of possession in the opening stages, but struggled to create any convincing chances against the stubborn Victory defence.
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Phoenix thought that they had taken the lead just before the 15-minute mark, after they placed the ball in the back of the net only to be disallowed straight after, when Leigh Broxham's strong challenge brought play back moments before.
However, Phoenix were not to be denied five minutes later, as Krishna broke the deadlock from the tightest of angles, slipping the ball over the line after controlling a deflected shot inside the area.
Melbourne responded quickly to the goal, not giving the hosts an inch to play their football, while churning out some of their own chances midway through the first 45 minutes.
Just as the visitors looked to be getting themselves back into the game, Phoenix struck again through Bonevacia on the stroke of half time, after Krishna slipped through the winger to thump the ball past Danny Vukovic in the Melbourne goal.
Victory needed an early second-half goal to have chance of getting back into the game but were thwarted each time by the home side's defending.
The visitors kept on pressing for their first goal of the match, but failed to come close to making the score 2-1, as the game sneaked towards full time.
Wellington held on to pick up all three points and claim a 2-0 win, as they move up to sixth, two points behind their opponents, who stay in first.