Baroka were out the starting blocks from the word go, giving the Soweto giants little breathing space to get into the game.
They provided an early scare when Robin Ngalande got behind Erick Mathoho to trigger an acrobatic save from Itumeleng Khune after 11 minutes.
The home side continued to pile on the pressure, forcing the visitors to concede countless corner kicks in the first half.
They nearly profited from one of them, but captain Olaleng Shaku failed to connect properly to head the ball on target.
They made amends on the half-hour mark when Lucky Nguzana tapped in after Talent Chawapiwa’s shot came off the post, leaving Khune stranded.
George Maluleka, who scored in the first round fixture between these two sides, tried to get on the score-sheet again but he shot tamely at Virgil Vries.
Ryan Moon came close with a header 10 minutes before the break, but it went wide of goal following Maluleka’s delivery.
Chiefs drew level a minute into the second half through the head of Moon following Siphiwe Tshabalala’s delivery.
Bakgaga looked to regain the lead and made two changes in Richard Matloga and Gift Motupa, while Nguzana was looking for his second after he intercepted from Mathoho but shot straight at Khune.
The Amakhosi were looking to take the lead for the first time in the match, but battled to get shots on goal despite the best efforts of Gustavo Paez and Maluleka.
New signing Leonardo Castro got a standing ovation as he was introduced in the 68th minute. However, the Amakhosi were dealt a blow soon after when Joseph Molangoane got his marching orders for an off-the-ball incident involving defender Khutso Mohwatseleng.
After a few attempts on goal, Castro finally introduced himself to the Amakhosi faithful with a first-time finish inside the box seven minutes before full time.
The win was Amakhosi’s very first against the Limpopo side, who got the better of them in the reverse tie.