The home side gave a start to Ayanda Dlamini in goal, with Rodwell Chinyengetere and Tshiamo Masiya, with Moses Spandeel and Rudiger Gilbert starting for the visitors.
Lions could've taken the lead just after the 20th minute mark, but Spandeel failed to connect with a cross from the right as the home side struggled to hold their lines.
The hosts soon gathered steam and inside the 23 minutes saw Clinton Davids tip Evidence Makgopa's close-range effort onto the top of the woodwork.
Lions grabbed the lead ten minutes to the break after Gilbert's free-kick deflected off the head of Sbonelo Ngubane before hitting an unguarded net.
Dylan Kerr looked for inspiration off the bench and introduced Ivan Mahangwahaya and Tshediso Patjie, who replaced Masiya and Mogau Khwinana.
Bakgaga Ba Ga Mphahlele levelled matters two minutes after halftime after Davids helped Makgopa's near post strike into the back of the net.
Gerald Phiri Junior worked a bit of magic towards the area at the midway stage and brought Davids to a reactive block with the defence rooted.
Either side found chances to go further ahead following the final quarter, but the finishing proved disappointing –thus steering the clash to extra time.
Lions were back in the driving seat seven minutes into extra time after Ethen Sampson tapped a low cross from the right into his own net.
Parity was restored a few minutes later after Manuel Kambala's low shot from the edge of the area went through the hands of Davids.
No goals arrived thereafter and the match was settled on a penalty shootout which Bakgaga bagged with four successful conversions after Lions missed three of their kicks.
Baroka: Dlamini, Makume, Makgopa, Kambala, Sampson, Phiri, Khwinana, Chinyengetere, Ngubane, Gerbhardt, Masiya.
Subs: Kazapua, Maloka, Mahangwahaya, Patjie, Chivaviro, Kgoetyane, Selemela.
Lions: Davids, Tau, Nkosi, Monaheng, Maritshe, Ramatlapeng, Gilbert, Nkosi, Spandeel, Arends, Rapatsinyana.
Subs: Sambo, Johannes, Chimuku, Borias, Mzimase, Maqhina, Mabena.