Ndivhuwo Ravhuvali broke the deadlock from the spot in the 52nd minute after Richard Matloga was fouled in the box.
Matloga then added a second goal in the 75th minute to help his team snap a 15-game winless run in all competitions.
Bakgaga, who are propping up the the Absa Premiership standings, notably fielded new signing Letladi Madubanya, who joined the club this week as a free agent following his exit from Platinum Stars last year.
FC CT: Khoza, Molomo, Kuilong, Gwala, Ndlovu, Chiwunga, Ndzie, Hleleni, Sambok, Hahn, Chivairo.
Baroka: Masuluke, Mapetho, Matloga, Shaku, Masenamela, Mahashe, Letsoalo, Ravhuhali, Kgaswane, Kunene, Madubanya.