After a closely fought 57 minutes on Saturday night, skipper Alex Brosque and Bobo cracked the game open with a goal each in a telling six-minute period.
The Brazilian striker sealed the victory with a second goal in the 90th minute.
One week after securing the Premiers' Plate with three matches remaining before the finals, the Sky Blues also kept a record 15th clean sheet for the season.
The three points takes the Sky Blues to 62 points, keeping the title favourites on track to shatter Brisbane's 65-point mark set over 30 games in the 2010-11 summer.
For City, the result leaves them hanging onto third spot alongside Brisbane Roar, who take on Central Coast Mariners on Sunday, and two points ahead of the in-form Western Sydney Wanderers.
Just days after his 20-minute cameo for the Socceroos, star Tim Cahill started but failed to get a shot off before bowing out in the 77th minute.
Played at a finals-style pace in front of the 15,266 at Allianz Stadium, it was a Bruno Fornaroli seventh-minute free kick that was the best chance for either side early on.
His inswinger beat the oustretched arms of a diving Daniel Vukovic but struck the post.
Aaron Calver also saved a Rhyan Grant blunder midway through the first half, while Fornaroli's ambitious scissor-kick wasn't far off.
City's chances seemed to kick the home side into gear, with a Bobo header just clearing the crossbar, as did Milos Ninkovic's dipping shot from outside the box.
Grant should've broken the deadlock after halftime when his close-range tap-in was saved off the line by Ivan Franjic, however it didn't take much longer for Sydney FC to seize the initiative.
And the opening goal came with shocking ease, with a long throw from Michael Zullo allowed to bounce by City and latched onto by a cutting Brosque.
Bobo doubled their advantage soon after, hitting home a low cross from Zullo from close-range and then completed a brace by nodding home a David Carney lob in the final minute.
