An 85th-minute penalty by Valere Germain - his fourth goal of the Cup campaign - proved enough for the visitors, who will face 2015 and 2021 champions Melbourne Victory in the decider.
For the Bulls, it offers a chance at not only a trophy but also the opportunity to look beyond an off-season marred by an alleged bet-fixing scheme involving former players Ulises Davila, Kearyn Baccus and Clayton Lewis.
"We've been through a lot, but everyone's working hard to make the club a success,'' said coach Mile Sterjovski.
"We want to be a success, we want to build the club as much as we can, and being in the final definitely helps."
Sunday's contest appeared destined for extra time, only for Lucas Inglese to collide with Jake Hollman as the two contested a high Liam Rose delivery into the box. Germain duly stepped up to score from the penalty spot.
But the French attacker won't be part of the final after being dismissed for a second yellow card in the 97th minute.
Valere Germain scored the winning penalty, but he will miss the Australia Cup final. (Joel Carrett/AAP PHOTOS)
"It's going be a big loss, but I have faith in my boys," Sterjovski said.
"We're looking forward to (the final), it's a great achievement for the club to be in the final again."
Seeking to become just the second side from outside the A-League to qualify for a final - Macarthur defeated Sydney United in the 2022 decider - South started well when Max Mikkola forced Filip Kurto into a close-range after just three minutes.
The Pole would prove the busier of the two keepers across the opening half.
South were obviously feeling the loss of their talisman Harrison Sawyer, the striker having signed for Macarthur midweek and unable to feature on Sunday.
And playing in their 39th competitive fixture of 2024, the semi-professional outfit faded as the second half progressed.
Desperation reinvigorated the hosts' efforts to grab a late equaliser, but it proved to be in vain.
The date and venue of the final will be announced soon by Football Australia.
