It was just City's second win of the campaign, their previous victory having also come at the expense of the reigning champions away from home in Round 5.
The result saw the Roar's brief upturn in fortunes under interim coach Frans Thijssen come to an abrupt halt, the title-holders having drawn one and won one with the Dutchman at the helm following the sacking of Mike Mulvey last month.
Familiar problems remain for both sides, with City guilty of missing several chances to put the outcome beyond doubt, while Brisbane - missing star playmaker Thomas Broich as he recovers from ankle surgery - failed to mount a meaningful threat on the opposition's goal.
In an indictment of the general standard at the wrong end of the table this season, City's victory takes them ahead of the Roar and into the top six, with the battle for the last finals berth thus far proving to be a race to the bottom.
What They Said:
"I got touched. I felt contact, so..." Mate Dugandzic defends himself from suggestions the penalty was soft.
Goals
1-0 (Mooy pen, 49')
Mate Dugandzic got in behind Daniel Bowles down City's left, advanced into the area and the Roar fullback made the mistake of putting his hand on the forward's shoulder. Dugandzic needed no further encouragement to go down, with referee Shaun Evans pointing to the spot and Aaron Mooy coolly tucking away the penalty.
Key moment
David Williams, on as a substitute at half-time in place of Damien Duff, should have made it 2-0 in the 53rd minute, putting a shot wide under no pressure following a good run into the box and lay-off from Dugandzic. Two minutes past the hour mark, Jacob Melling was also guilty of a bad miss, firing over from inside the area after good build-up play by Dugandzic and Williams.
Opta Data key stats
The visitors had just one shot on target in the match, Matt McKay missing their two most presentable opportunities in the first half, blazing one wide and hitting the crossbar with the other. After that Thijssen's men looked toothless, worryingly so for those of an orange persuasion.
Highlights reel
Melling took the Roar defence out of the equation with a piercing delivery to Mate Dugandzic on the opposite flank in the 75th minute, but nothing came from the eye-catching show of precision.
The Final Word
Next up for the Roar is a tough assignment away to in-form Adelaide United on Friday night, while City, with no match next weekend, have something to build on during their wait to face Melbourne Victory in the derby on December 20.
Teams
Melbourne City: Velaphi, Hoffman, Chapman, Kisnorbo, Garuccio, Paartalu, Mooy, Melling (Murdocca 85'), Duff (Williams, 46'), Brown (Ramsay, 75'), Dugandzic.
Brisbane Roar: Young, Brown, North, Smith, Bowles, McKay, Brattan (Lustica, 78'), Kurtisi (Solorzano 67'), Borrello (Sarota, 63'), Henrique, Petratos.
Scorers: Mooy, penalty (49')
Red cards: None
Yellow cards: Bowles 32'
Conditions: 22 degrees, rain
Attendance: 7, 721 @ AAMI Park