Kaizer Chiefs went ahead when Gaston Sirino beat Orlando Pirates goalkeeper Sipho Chaine from the penalty spot 10 minutes into the contest.
This was after Deano van Rooyen was adjudged to have tripped a charging Pule Mmodi inside the box.
But Evidence Makgopa replied for the Buccaneers seven minutes later by heading in a Deon Hotto freekick.
Seven days earlier, Makgopa was on target for Pirates to equalise in a Premier Soccer League Soweto Derby, which the Buccaneers went on to win 2-1.
But this time his goal counted little as Chiefs reclaimed their lead with 10 minutes remaining when Yusuf Maart volleyed home after being set up by Ashley du Preez.
It was a memorable evening for Nasreddine Nabi's Chiefs, who won 2-1 and lifted a major trophy for the first time since 2015.