Chiefs introduced a few changes, notably in goal with Virgil Vries replacing Itumeleng Khune in a total of seven alterations by Giovanni Solinas.
There was no shortage of drama at the start, with Leopards threatening an early lead but Vries quickly thwarted the danger.
The hosts created their own worthwhile chance but Hendrick Pule Ekstein shot tamely at King Ndlovu on six minutes.
Lidoda Duvha made another opportunity and Mwape Musonda missed the net by a whisker on 12 minutes.
Zimbabwean Willard Katsande squandered a glorious opportunity inside the box when he curled over the top from just five metres.
Zambian-born Musonda then rattled the crossbar after 24 minutes following a glancing tap inside the box.
The visitors stunned the hosts through a stunning finish that trickled the underside of the bar and into the net by Phathushedzo Nange.
The Amakhosi threw bodies forward just before the break and Bernard Parker was denied by the post after striking from range.
In the second half, the home side started with the expectancy to grab the equaliser but struggled to break down the defensive block.
Leopards were content to play it out on the counterattack and crept up a few half-chances. The Soweto side grabbed the equaliser after Ekstein brought down a long ball to squeeze past Ndlovu.
Substitute Ryan Moon tried to give them the lead but his glancing header failed to properly test Ndlovu.
Leopards nearly regained the lead and it needed expert goalkeeping from Vries to acrobatically deny Musonda from close range.
With extra time looming, chances at both ends appear and Moon fired wide of the upright whilst Jean Munganga headed off target from a corner.
Ndlovu kept Leopards in with a chance after denying Kabelo Mahlasela from point-blank range as the only meaningful chance happened in the second half of extra time.
The post denied the Amakhosi for the second time this time with Katsande’s powerful shot from a distance.
Leopards had the side-netting with a shot from Tshepo Hlongwane after a square pass from the right as the game went to penalties.
After successful three conversions, both sides then missed with Munganga and Godfre Walusimbi. Mthokosizi Nene then missed another for Leopards, allowing Moon to convert the final kick to give the Amakhosi the victory.
Chiefs: Vries, Mphahlele, Mathoho, Booysen, Walusimbi, Ekstein, Katsande, Ntshangase, Zulu, Parker, Páez.
Subs: Khune, Cardoso, Ntiya-Ntiya, Maluleka, Jayiya, Moon, Mahlasela.
Leopards: K. Ndlovu, Munyai, Zulu, Munganga, Katjiukua, Nange, Mhlongo, Nene, Musonda, Kapinga, Hlongwane.
Subs: Muleka, Ndou, T. Ndlovu, Khutlang, Mokoena, Tshepe, Mahangwahaya.