City emerged 3-2 winners from a pulsating match which swung in the breeze before settling in favour of John van ‘t Schip’s side.
First half strikes from Novillo and golden boot leader Bruno Fornaroli set City on their way.
Two gaffes either side of halftime allowed the Wanderers to regain parity.
Mitch Nichols rasped a volley through City keeper Thomas Sorensen’s fingers before Aaron Hughes scored an own goal from Romeo Castelen’s tricky cross.
But in a match played in full voice, it was Novillo’s shout that mattered most.
With just five minutes remaining, the winger rescued a lost ball and curled home past former City keeper Andrew Redmayne.
The match reinforced the gains made by John van ‘t Schip’s side this season.
In the same fixture in November, City were swatted aside in a 3-0 loss that left them outside the top six.
Since then, van ‘t Schip’s side have won five of seven matches to sit third and now must be thought of as genuine title contenders.
The Dutchman showed his tactical nous by continuing a new formation with three at the back and moved Novillo up front with Fornaroli.
By the half-hour mark, both had goals.
A handball from Nikolai Topor-Stanley on the edge of the box brought both Aaron Mooy and Novillo around the set piece.
The Frenchman took four steps and planted it beyond Redmayne, who endured catcalls all night after struggling with his distribution.
On 24 minutes, City made it two after Sorensen and Mooy fed Fornaroli in a lightning-quick transition.
The Uruguayan had plenty to do but bought enough space between Scott Pepper and Andreu to curl past Redmayne for his 12th goal of the season.
Against the tide, Western Sydney had a reply five minutes later.
Mark Bridge’s opportunistic lob gave Nichols a one-on-one chance, which the in-form playmaker struck with full venom.
The ball dipped enough to slip past Sorensen and into the net, a rare mistake from the veteran Dane since his Australian move.
Tony Popovic hauled off marquee striker Federico Piovaccari after less than an hour, and within a minute his replacement left his mark.
Castelen fizzed a cross from the right that Hughes couldn’t leave alone and toed unfortunately into his own net.
The Wanderers were in the ascendancy, with Sorensen keeping City on terms with a fabulous double save from Castelen and Bridge.
Both sides swapped golden chances before Novillo emerged to win it and ending Western Sydney’s 10-game run without loss.
Van ‘t Schip said while the Wanderers had them under pressure for long periods, he felt a good energy around AAMI Park.
“We’re showing progress,” he said. “We’re getting stronger as a team.”
Popovic rued a Bridge goal that was disallowed with the score at 2-2.
“We’ve had no explanation, I don’t think we need one,” he said.
“He blew the whistle to play, we played and we scored. That’s it.”