Danny Allsopp scored two first-half goals as the Victory went into the break 2-1 up after reliable striker Shane Smeltz netted once again for the home side, giving them a glimmer of hope.
Victory's Brazilian import, Ney Fabiano, opened up his scoring account for his new club just after half-time before Smeltz came to the rescue again with a 64th minute penalty.
The game was then put to rest however when Kevin Muscat converted from the penalty spot just a minute later.
Melbourne jumps to the top of the table with the impressive performance while Wellington find themselves on the bottom after their draw in Round 1.