Phoenix had never won in Melbourne, and that seemed further away than ever when former winger Marco Rojas and Marcos Flores put the hosts two goals to the good by by half-time.
Another Rojas goal looked to seal Victory's second success of the season, before Phoenix staged a late fightback, featuring Jeremy Brockie's outstanding double.
The hosts had stand-out performances across the pitch, but it was a result largely built on the craft of Flores and Guilherme Finkler.
Signs that better times are ahead for Victory were there from the eighth minute, when Finkler and Flores combined in midfield for the former to guide a through ball into Archie Thompson's path but his shot went wide.
Thompson had his second chance when Mark Milligan's lightning ball across the goalmouth just evaded him on 15 minutes, while Phoenix replied seconds later after Louis Fenton's superb ball from the right curled just past Stein Huysegems.
Victory took the lead in the 23rd minute when Finkler's through ball found Thompson wide on the right. Presented with a one-on-one chance with Mark Paston, the Australia international instead elected to send a perfect ball across the goalkeeper and two defenders for Rojas to tap home.
Thompson and Brockie then brought saves out of their opposing goalkeepers, before Flores put Victory further ahead seven minutes before half-time.
Retrieving the ball from the right, Flores and Finkler traded two passes apiece before the former finished with the outside of his right foot.
The second goal had been coming, but few of the 20,683 crowd could have predicted its quality.
One minute into the second half, Milligan's ball ensured Thompson again found a galaxy of space behind the Phoenix defence, and his precise ball across goal ensured an easy tap in for Rojas.
Application had not been in question for Thompson over a 13-game scoreless streak in the A-League, but he again showed his finishing was still somewhat off when he spooned a cut-back from Flores high and wide from close range on 51 minutes.
Meanwhile, the injection of Benjamin Totori for the Phoenix proved crucial to their attempts to save the game.
The Solomon Islands international was integral in the Phoenix's brightest spell of the game, which produced Brockie's first goal in the 81st minute.
He sent an unstoppable shot past Nathan Coe from outside the area after having been fed by the increasingly lively Totori, and then made it a double when his free-kick was clawed out by the Victory goalkeeper only after it crossed the line.
But time beat Phoenix, with Victory's win certainly not the most impressive of the weekend but it did provide 60 minutes of exactly what they are capable of producing under coach Ange Postecoglou.