There was a hint of controversy to the goal as there were questions around whether Thompson was onside, while it also looked to have taken a deflection off Phoenix skipper Andrew Durante.
With their tails up, the Victory ran rampant as they exposed the Phoenix down the flanks and through the middle of the park.
Phoenix right back Louis Fenton, who has been converted to a defender in the off-season by Merrick, was at sea during the early stages of his first start of the year after recovering from a recent shoulder injury.
But for all of Fenton's troubles, it was Durante who provided a rare mistake, which led to the Victory's second.
The All Whites defender tried to head a ball back to Moss in goal but didn't get enough on it and only succeeded in rolling it in to the path of Victory midfielder James Troisi, who finished with ease in the 20th minute.
Before the half-hour mark, the Victory were up 3-0 when Troisi, who is in Melbourne on loan from Italian Serie A club Atalanta, beat Durante to the ball and produced a creative finish over an oncoming Moss.
Down 3-0, the game looked done for the visitors but Jeremy Brockie gave Wellington a lifeline when he scored only six minutes later as an open first-half continued in hasty fashion.
Phoenix striker Stein Huysegems then had the ball in the back of the net in the 40th minute but his effort was correctly ruled offside.
The second spell started with much of the same for Melbourne as they were dominant for the first 10 minutes before Wellington started to mount any resistance.
Merrick went to his bench mid-way through the second spell as substitutes Jason Hicks, Paul Ifill and Leo Bertos floated in to the game.
The Victory seemed comfortable with their lead as they dropped off during the second half and when Ifill found the back of the net in the 84th, it was game on.
But three goals proved too many to come back from as Wellington couldn't find a late equaliser and the Phoenix remain anchored in ninth on the A-League ladder after four rounds.
Melbourne Victory 3 (Archie Thompson 8, James Troisi 20, 29) Wellington Phoenix 2 (Jeremy Brockie 35, Paul Ifill 84) Halftime: 3-1