The 20-year-old winger, on loan from Danish club Brondby, snatched a goal and two assists in a dazzling display - before souring the night by picking up a second yellow card in the 67th minute at AAMI Park on Saturday night.
Younis was booked for taking out Lawrence Thomas in the 13th minute, then received a second yellow card for catching Alex Gersbach in the lower leg.
Fourth official Jonathan Barreiro alerted referee Lachlan Keevers to the foul.
It rules Younis, who has nine goal involvements in 11 games across all competitions, out of Tuesday night's clash with Central Coast.
"It was a good performance from Marcus. He's been really good for us since he's been here," Vidmar said.
"The red card - I don't know why the fourth official needs to get involved with the decision. The ball's trying to go over his head, he doesn't even know where his opponent is and he's just trying to grab the ball.Â
"They told us he kicked him in the calf - and it was nowhere near his calf. So for me and I think for everyone it was a wrong decision and hopefully that doesn't hurt us."
The victory, which lifted the reigning champions up to seventh, just two points behind sixth-placed Macarthur FC, came at a cost, with City midfielder Ryan Teague substituted at halftime with a left knee injury.
The bottom-of-the-table Wanderers are winless in four matches ahead of next Saturday's derby against Sydney FC.
Days after ex-Sky Blues boss Ufuk Talay was announced as incoming manager for next season, regulars Brandon Borrello, Ryan Fraser, Kosta Barbarouses, Hiroshi Ibusuki and Jacob Farrell weren't in the team.
Interim manager Gary van Egmond insisted their absences weren't related to his previous comments that the Wanderers squad needed a "giant overhaul".
"They're all injured at this moment," he said.
"Brandon's got a slight tweak in his groin. Ryan's got a tight achilles. Kosta, it's his calf. Hiroshi's coming back from a calf.
"Jacob Farrell - groin - and we'll probably be lucky to see Jacob back this year."
City were without first-choice goalkeeper Patrick Beach, who picked up a quad injury on Socceroos duty, and James Nieuwenhuizen debuted.
Western Sydney spurned three gilt-edged chances in the opening six minutes, and City's Daniel Arzani fluffed two before the hosts broke through at AAMI Park.
In the 23rd minute, Younis slipped through Andreas Kuen, who spun through traffic then coolly finished into the bottom corner.
Younis scored 10 minutes later when he let rip from long range and his strike took a nasty deflection to beat Thomas.
Four minutes after halftime, Elbasan Rashani latched on to a Younis cross to wrap up three points.
