Luyando Nomandela had given Stars an early lead, but second half strikes from Lyle Lakay and Lennox Bacela saw Siwelele through.
After a quiet start the opener arrived on 19 minutes when Nomandela controlled a high pass from Dove Wome before beating Patrick Tginyemb with a low finish.
The visitors almost leveled on 36 minutes when Daniel Cardoso failed to clear inside the box, but Joel Mogorosi curled his shot wide.
Wome almost added to the lead early in the second half but he was denied by an excellent low save from Tignyemb.
It proved crucial as the equaliser came soon afterwards when Lakay beat Kennedy Mweene with a long-range shot.
Tignyemb again denied Nomandela, before the striker fired narrowly wide of the post five minutes from time.
The miss proved costly as Bacela shrugged off a defender before racing into the box and firing past Mweene to see his side through.