A win would've put them in a great position to claim third spot from Perth, which would give them two home games in the post-season.
Finishing fourth would give them an all-important home tie for the first round of the playoffs, although two losses to finish the season could see them slip to fifth or sixth where they would be forced to go on the road for a knockout clash.
Melbourne on the other hand, despite their plethora of talent, are out of playoff contention and are only playing for pride during the remaining games of the season.
Despite coming in to the game with only five wins to their name this season, Melbourne could boast that two of them were over the Phoenix.
The visitors welcomed back All White Leo Bertos in to their line-up and the winger began the game from the bench but joined the fray on the hour mark with forward Mirjan Pavlovic as the Phoenix tried to force their way back in to the game.
Alex Smith was the only change to the starting XI from the side that drew 1-1 with the Melbourne Heart last week as he replaced former Victory midfielder Nicky Ward.
Ward joined the game to a chorus of boos with about 20 minutes left when he replaced Spanish midfielder Dani Sanchez.
Former Phoenix attacker Marco Rojas started the game for Melbourne but didn't last long after he collided with Manny Muscat and the Kiwi international was substituted with concussion-like symptoms before 20 minutes had elapsed.
The Victory made three changes for the game in all, which included the return of the dangerous Hernandez from suspension.
Archie Thompson, who hadn't scored in his past nine A-League games, looked certain to score in the first half but could only find the woodwork in the 32nd minutes as his drought continued.
The Phoenix round out the regular season when they host the league-leading Central Coast Mariners at their Westpac Stadium fortress on Sunday, March 25.
Central Coast will hold no fears of travelling to Wellington after they beat the Phoenix 2-1 in New Zealand's capital in November.
Melbourne Victory 3 (Carlos Hernandez 11', Isaka Cernak 55', James Jeggo 89') Wellington Phoenix 0 HT: 1-0