The 19-year-old followed his own cross from the left into the box and lashed his low shot through the legs of a defender and an unsighted Moss to give his side a deserved lead.
Phoenix had been playing with great endeavour without giving Victory keeper Nathan Coe too much to do and their work was rewarded with a brilliant free kick from Rolieny Bonevacia in the 42nd minute.
With the Victory wall standing on the edge of the box, the Dutchman curled his shot into the top left corner to send the sides into halftime deadlocked.
Victory turned up the heat after the break and deserved to go ahead once more in the 53rd minute when Barbarouses coolly converted from close range after being set up by Carl Valeri.
But with the champagne on ice, Muscat's men were inexplicably unprepared for a set piece in the 68th minute when Michael Boxall wandered in behind their defence to head home a Bonevacia free kick.
The scene appeared set for Thompson when he was subbed on in the 73rd minute, but a quick counter-attack by Phoenix again caught Victory napping with Boxall squaring the ball to Burns who scored with the simplest of tap ins.
With the home crowd in full voice, Victory pressed hard but couldn't find a way through as Ernie Merrick's side held on for a memorable win.