The Phoenix were down on manpower for the game as it was, with Paul Ifill still battling a groin injury and Muscat suspended from his red card in the last game against Perth.
Dani Sanchez got the Phoenix on the board in the 71st minute as the home side battled valiantly with only 10 men but they couldn't find a late equalizer.
Former Phoenix favourite Marco Rojas started as substitute and when he walked out to take his place on the bench he was subjected to chants of "Judas" from the Yellow Fever faithful.
Rojas, entered the game in the 64th minute to jeers and boos from the home crowd, who are clearly still smarting from the youngster's decision to leave Wellington at the end of last season.
Despite all their big-name recruits such as former Liverpool star Harry Kewell and Rojas to team with Thompson and Hernandez, the Victory came into the game yet to score a goal in their opening three matches.
Thompson broke the deadlock when he danced past Nikolas Tsattalios and placed a shot neatly in the right-hand corner of Tony Warner's goal in the first half.
In the opening 20 minutes the Phoenix missed three golden chances, with Sanchez the worst offender.
The Spanish midfielder pushed a good opportunity wide of the the post in the 11th minute then six minutes later knocked a header wide of the mark from point blank range.
Leo Bertos failed to latch onto a great cross from Daniel as the Phoenix made plenty of inroads down the left side of the park.
All Whites midfielder Tim Brown also failed to take advantage of another prime scoring opportunity after 25 minutes when he put his shot from inside the box over the crossbar.
During the opening spell the Victory attacked in spurts but failed to string together large periods of dominance, while the home side battled to provide support for lone Phoenix striker Chris Greenacre.
Melbourne Victory 2 (Archie Thompson 42', Carlos Hernandez 67' pen) Wellington Phoenix 1 (Dani Sanchez 71'), HT: 1-0