City will meet Sydney FC in the final at AAMI Park on November 30.
City prevailed in a brutally physical semi-final, thanks to goals from Luke Brattan and Fernando Brandan.
There were numerous clashes between individual players throughout the match, including a heated argument between Tim Cahill and Kevin Muscat during the first half.
Brattan opened the scoring in the eight minute in controversial circumstances as the goal was originally ruled out, before the referee overruled his assistant.
As Brattan launched his shot from 25 meters out, Cahill was in an offside position, but the Socceroo attacker managed to duck out the way as the ball whistled past his back, Lawrence Thomas' out-stretched hand and into the back of the net.
The assistant referee raised his flag, but the referee ruled that Cahill was not interfering with play or impeding Thomas' view and the goal counted.
Victory boss Kevin Muscat railed against the "staggering" call after the match.
"Timmy has to get out of the way otherwise it's going to hit him ... if you have to get out of the way of the ball travelling towards the goal I'd suggest you're obstructing the keeper," he said.
City sealed the victory after pouncing on a Nick Ansell error, who was disposed on the edge of his own penalty box. The ball spilled to Nick Fitzgerald whose deflected shot fell into the path of Brandan who scored his third goal in as many matches.
Unlike their A-League duel of 10 days ago, City were made to work for this win.
The fight was on from the first whistle.
Every foul seemed to bring either an argument or a scrap and none were bigger than when 17-players came together after Cahill wrestled Leigh Broxham and Rashid Mahazi to the ground in the fourth minute.
Both sides were desperate to gain the upper hand from the get-go, having seen City prosper from a brighter start in their last meeting.
Cahill's close-range shot was then saved by Thomas but City had their opening goal shortly after through Brattan.
Dean Bouzanis - surprisingly kept in goal despite his howler in City's last-out loss - struggled with distribution and was baited by Besart Berisha for every mistake.
The Albanian turned villain on the half-hour mark, spooning Marco Rojas' pinpoint cross over the bar when an equaliser beckoned.
Michael Jakobsen was forced to clear a Victory header off the line as Kevin Muscat's side rose to the challenge.
Rojas was inspiring his side back into the contest, and raced clear to tee up Broxham, whose deflected shot fizzed agonisingly wide.
The Kiwi had the ball in the back of the net in the 72nd minute but unlike City, weren't afforded the benefit of the officials' doubt.
Instead, City - who were deserved winners on the night - made sure of their maiden finals appearance when Brandan scrambled an effort home to capitalise on Victory's indecision in defence.
City coach John van 't Schip said he was delighted to see his side take up the physical challenge once more to Victory.
"We knew that there was going to be a lot of emotion, especially after the last game ... they were fired up," he said.
"They showed they were out there to get a result (but) that's the quality of our team. We can match that."