Amakhosi, who won the competition last year, reached the final after beating ABC Motsepe League side ABC Motsepe League 2-0 in the first semifinal.
Ea Lla Koto beat Chippa United 3-1 in penalties after the match ended goalless.
Chiefs took the lead in the 29th minute when debutant Khama Billiat’s cross was volleyed home by Leonardo Castro at the far post.
Harris Tschilbou should have equalised for Stars on the hour mark, but his effort was tipped away by Virgil Vries.
Ea Lla Koto managed to get their equaliser in the 82nd when substitute Eleazar Rodgers beat Vries from the penalty spot.
Chiefs claimed a 6-5 win in the shootout in the end to clinch the Maize Cup.