The win has returned Melbourne to the top of the table, three points clear of 2nd placed Gold Coast United who play later on this weekend.
The home side went into the clash without Archie Thompson and Kevin Muscat but were still considered hot favourites to defeat Robbie Fowler's Fury side.
The Victory dominated possession in the first half, with the Fury starved of the ball but bad news presented for the Victory with what looked like a serious knee injury to Matthew Kemp after 11 minutes.
Melbourne had to wait until the 35th minute to take the lead, with Hernandez collecting the ball on the byline before cutting back and slotting home from a tight angle.
The Fury had chances late in the first half, the first to Beau Busch and the next to Robbie Middleby.
After the interval the play opened up with both sides having scoring opportunities. New signing Nick Mrdja was looking dangerous up front for the Victory whilst Fury midfielder David Williams, who came on as a substitute, was making an impact.
Hernandez, who's 20th minute freekick had crashed against the crossbar, settled the scoring in the 66th minute with a brilliantly taken freekick which gave Justin Pasfield no chance.
The Fury had several late scoring chances, whilst Mrdja crashed a seemingly easy opportunity against the crossbar in the dying minutes.
The result ends Fury's hopes of a finals spot.