The Bulls took the lead at Campbelltown Stadium through a Jed Drew goal in the fourth minute of added time in the first half and held on in front of their biggest ever home crowd of 7723.
The win, Macarthur's first at home against Sydney in four attempts since they joined the competition in 2020, lifted them above their opponents into fourth.
They are three points clear of their local rivals heading into next week's final round.
Macarthur had defenders Ivan Vujica (37th minute) and Tommy Smith (65th) sent off, each after involvement from the VAR following an initial yellow card.
Vujica caught Sydney winger Joe Lolley on the ankle, although it didn't appear a particularly dangerous or malicious tackle.
New Zealand International Smith raised his arm and caught Sydney's Brazilian striker Fabio Gomes in the face.
But VAR intervention finally favoured the Bulls when a potential Lolley equaliser in the 75th minute was rubbed out for offside.
Sydney rained in lots of shots throughout the second half, but Macarthur goalkeeper Filip Kurto pulled off some good saves and the lacklustre Sky Blues had numerous off-target attempts.
Even with reduced numbers Macarthur posed the occasional attacking threat, but it was their defensive resolve which secured the win.
