Victory look all but certain for the finals after putting a six point gap between them and seventh placed Sydney FC, who have three matches remaining, meanwhile league leaders Western Sydney look destined to be leapfrogged by the end of the weekend.
Kevin Muscat had called for an improved performance after an "unacceptable" match against Newcastle Jets last week, and his players obliged instantly.
Oliver Bozanic scored with a powerful low drive in just the second minute, that seemed to catch Wanderers 'keeper Liam Reddy by surprise, to give Melbourne an early lead.
It was an intense match throughout with both sides struggling to create chances in the first half due to the intense pressing of both teams in midfield.
Melbourne were very lucky not to be down to 10 men in the 43rd minute when Daniel Georgievski went flying in with a knee-high challenge on Mitch Nichols. The Macedonian thankful to only receive a yellow card, while Nichols walked away thankful to be able to do so.
The Wanderers started to gain more control in the second half, but failed to convert that possession into shots on goal. Fahid Ben Khalfallah especially good in tracking back and winning possession for his side - he did so 11 times, the second highest of anyone on the pitch.
Melbourne started to create more chances on the counter-attack and in the 66th minute made it 2-0 thanks to Bozanic.
The defensive-midfielder made the most of a fortunate deflection that fell straight into his path before toe-poking the ball past Reddy.
Muscat was savouring a first home A-League win in two months he felt was "fully deserved".
"We showed a lot of endeavour. We showed a lot of mental strength to perform at that level," he said.
Popovic said his team played well in the first half but the early goal boosted Victory.
"They've been down a little bit on confidence and that maybe gave them a lift," he said.
"Goals do change games. Unfortunately we couldn't take those good opportunities we had."