City striker Bruno Fornaroli continued his rich vein of form, turning Manny Muscat inside out before bending a curling effort past Glen Moss in the 12th minute to slot home his 13th goal of the season.
Harry Novillo doubled Melbourne's lead after 30 minutes, meeting an immaculate Michael Zullo cross with a well-timed finish. He made the points safe just after halftime with a bullet into the top corner after some good City buildup.
Bonevacia was once again a bright spark in midfield for the Phoenix but quickly became frustrated that his team mates couldn't reach his high standards. The Phoenix will do well to keep hold of Bonevacia in the offseason as he appears to quickly be tiring of consistently being the best player in a losing team.
Ridenton at right back and Tom Doyle at left back both had nights to forget and were routinely terrorised by the exciting City attacking trio of Fornaroli, Novillo and Zullo.
But Bonevacia's wonder goal aside, the Phoenix never really looked like scoring. Since Roy Krishna got injured two weeks ago the Phoenix have failed to look dangerous in the attacking third and the drab reality for Phoenix fans is that they no longer have a goal scorer.
The Phoenix played like a team that belong in the bottom three and City appear to be a side ready to challenge for the title.
Melbourne City 3 (Bruno Fornaroli, Harry Novillo 2)
Wellington Phoenix 1 (Roly Bonevacia)