Thembinkosi Lorch, who sat out against Highlands Park, returned along with Makaringe and Kabelo Dlamini, while George Maluleka came in for the injured Reeve Frosler on the Chiefs side.
Maluleka looked to give Chiefs an early lead with a shot from the edge of the area after getting goal-side straight from kickoff, but Wayne Sandilands got behind the effort.
Samir Nurkovic thought he had put Chiefs ahead on 20 minutes after heading home Khama Billiat's delivery, but the striker's header was flagged offside.
Rhulani Mokwena's side were thrown into disarray five minutes from halftime after Mthokozisi Dube received a second yellow and subsequent dismissal following a foul on Billiat. Chiefs looked to make use of the man advantage as Ernst Middendorp brought in Bernard Parker, who replaced Njabulo Blom six minutes later.
Middendorp throwing in the kitchen sink paid fruits inside three minutes after Billiat's shot off the post landed kindly to Leonardo Castro who tucked into an empty net.
Pirates were close to falling behind three minutes to fulltime when Billiat's corner swerved towards goal, but Sandilands reacted quickly- leading the match to extra-time in the process.
Chiefs made a blistering start a minute in when Daniel Cardoso fired home from the spot after Abel Mabaso handled Eric Mathoho's volley.
However, Gabadinho Mhango levelled matters straight from introduction when he sliced through the defence to side-foot past Akpeyi ten minutes later.
No further goals arrived, as the Glamour Boys clinched victory in the penalty shoot-out with Parker netting the final kick whilst Pirates missed two kicks.
Chiefs: Akpeyi, Sasman, Mathoho, Cardoso, Blom, Katsande, Maluleka, Manyama, Nurkovic, Billiat, Castro
Subs: Bvuma, Parker, Kambole, Zulu, Zuma, Ngezana, Ntiya-Ntiya
Pirates: Sandilands, Dube, Jele, Maela, Nyauza, Motshwari, Dlamini, Makaringe, Pule, Lorch, Mabasa.
Subs: Delle, Chabalala, Mabaso, Mako, Mhango, Shonga, Mulenga