With scores level, Wanderers substitute Marcus Antonsson found the back of the net at CommBank Stadium with a header deep into added time on Saturday.
But his goal was chalked off after VAR found Anthony Pantazopoulos was offside.
While conceding Pantazopoulos had strayed offside, Stajcic insisted his player returned to an onside position before Antonsson made his header.
"They made the wrong call. Yeah, looks like it," Stajcic said.
"Marcus Antonsen got a flick-on and in that time it's hit Pantazopoulos, who by that time had got back onside because one of their players had dropped to the line.
"It's a legitimate goal."
The Wanderers desperately tried to rally before their counter-attack was called off by the final whistle.
"We're obviously disappointed to cough up a 2-0 lead," Stajcic said.
"But at the end of the day, it was a top match and fitting for both teams who played really well
"Two great sides, locking horns."
Second-placed City needed to defeat the Wanderers to stay within reach of the premiership plate after league leaders Auckland defeated Melbourne Victory earlier on Saturday.
A draw mathematically keeps Aurelio Vidmar's side in the premiers plate race, but their chances remain slim given Auckland have a superior goal difference (+23 to City's +12).
The Black Knights lead the league with 50 points, with City on 44 points ahead of the final two games of the home-and-away season.
Western United, after a shock 2-1 defeat to Brisbane earlier in the week, remain in contention for second on 41 points.
Vidmar insisted his side hadn't been focused on the premiership calculations going into the match.
"Tonight was probably the first opportunity where, had we won, we could have taken a giant step for that second spot," he said.
"In saying that, I think we showed a hell of a lot of character in that second half."
Western Sydney fumbled their chance to close in on a home elimination final, remaining fourth on 40 points.
A Nicolas Milanovic special had put Western Sydney in pole position to spoil City's party.
The 23-year-old opened the scoring in the ninth minute from the tightest of angles after Gabriel Cleur outmuscled Socceroos left-back Aziz Behich.
Milanovic popped up again four minutes later, dancing around defender Kai Trewin and Behich to find the back of the net.
The score was marked down as a City own goal after the ball was found to have deflected off Trewin's foot.
Trewin found redemption by pulling one back with a 36th-minute header after a Marco Tilio corner kick, before coolly converting a penalty in the 86th minute to level the scores.
"Someone mentioned he (Trewin) scored a hat-trick tonight," Vidmar joked.
The visitors had earned the penalty after Pantazopoulos downed Medin Memeti in the box in the 84th minute.
Milanovic goes to equal-second in the league's Golden Boot alongside Sydney FC star Adrian Segecic (12 goals), one goal behind Adelaide United's Archie Goodwin.
