The Victory, who did not have a shot on goal in the opening 45 minutes, closed the gap when Harry Kewell banged home the third penalty of the match in the 68th minute before the home side had the last say when substitute Andrezinho scored two minutes from time.
Between the fourth and fifth goals of the match Victory were reduced to 10 men when Danny Allsopp was sent off for a tackle on former Victory defender Steve Pantelidis.
He will miss at least Thursday's crunch match with Sydney FC.
Melbourne will go into that home game four points behind Sydney, who are in sixth place and holding the last play-off spot.
Magilton is hoping to bring fresh faces into the squad.
"I think what's happened here is they've got into a rut and I think the sooner we can change personnel I think the better," he said.
In winning two in a row on the road for the first time with their 1-0 victory in Newcastle, the Wellington Phoenix - winners of three of their last four outings - have dragged themselves into third place a handy eight points clear of the Victory, who sit one place outside the play-offs.
The Phoenix, after a nine-day break, are back at Westpac Stadium on Sunday to face fourth-placed Melbourne Heart in a game coach Ricki Herbert sees as crucial to their play-off aspirations, given it is one of only four at home in their remaining nine games.
The Heart dropped points in being held 1-1 at home by former league leaders Brisbane Roar. The Brisbane side are now a massive 11 points back from leaders Central Coast Mariners in second place and just two ahead of the Phoenix.
The Mariners followed last week's midweek 1-0 away win over the Heart with a tough 3-2 home win over Adelaide United, who play Newcastle Jets tomorrow.
Sydney FC made hard work of it at home against bottom-placed Gold Coast United.
Young Ben Halloran, who continues to impress, gave Gold Coast the lead after 55 minutes. The home side drew level through Karol Kisel 16 minutes later but did not get in front until two minutes from time when Bruno Cazarine scored.
Away from Thursday night's game between the Victory and Sydney FC and the clash between the Phoenix and Melbourne Heart, the contest between Adelaide and Perth holds most interest as the battle for play-off spots intensifies.