Troisi took his tally to four goals from three games as Victory handed Muscat his first win since taking charge last week
It was an unhappy return to an old stomping ground for ex-Victory pair Ernie Merrick and Carlos Hernandez, as the visitors from New Zealand found themselves 3-0 down within the first 30 minutes at Etihad Stadium.
The Kiwi side pulled a goal back in the first half and nabbed a second with six minutes remaining to make for a nervous finish to the game for the home side and their supporters.
But Victory survived to record their second win in succession and join Western Sydney Wanderers on eight points after four rounds of the 2013-14 A-League season, one point behind leaders Brisbane Roar.
Wellington are second from bottom, level on two points with Melbourne Heart.
Following a feisty start to the clash, Muscat's first in charge after succeeding the Socceroos-bound Ange Postecoglou, Victory opened the scoring in the ninth minute through Archie Thompson, who received a pass with his back to goal before turning and shooting beyond Glen Moss.
The final game of a round in which A-League match officials have come under major scrutiny for a series of poor decisions, Matthew Gillett and his assistants evidently had no desire to be left out, failing to spot a handball from Thompson which enabled the striker to create the opener.
Mid-way through the first half the home side doubled their lead, and this time the Phoenix had no-one to blame but themselves. Or, more specifically, captain Andrew Durante, who left an attempted header back to his goalkeeper well short, allowing James Troisi to steal in and finish with ease.
By the 30-minute mark Victory were 3-0 up, courtesy of Kosta Barbarouses' inch-perfect forward pass and an exquisite chipped finish from Troisi.
At that point the game looked dead and buried with an hour still to go, but five minutes later former Victory favourite Hernandez breathed life back into the contest when his slide-rule pass released Jeremy Brockie through on goal, and the New Zealand international made no mistake with a shot through Nathan Coe's legs.
The home side still appeared assured of collecting all three points, as a tame second half passed largely without incident.
That was until substitute Paul Ifill cut in from the right flank, beat Adama Traore and then Mark Milligan, before poking the ball between Coe's legs to make it 3-2.
But there was to be no dramatic escape act, and Merrick's search for a first victory in charge of his new club will continue until at least next week's game against Perth Glory in Christchurch.
Victory meanwhile have an enticing 'Big Blue' clash away to rivals Sydney FC to look forward to on Saturday, the next test of Muscat's fledgling tenure.