The clash headed into extra-time, where Baroka won a penalty with 10 minutes in. Mduduzi Mdantsane stepped up and scored.
Just when one thought Baroka had won, Thembikosi Lorch equalised for Pirates late on. However it was Lorch who missed the decisive kick in the shootout.
Here's how South African football fans reacted to this mighty upset on Twitter.
A former Kaizer Chiefs legend who played in a trophy winning era for them transfers this phenomenon and wins silverware as a Coach of @Baroka_FC #Legend— robertmarawa (@robertmarawa) December 8, 2018
1993 and 1994 winning the BP Top8 with them in 1994 as they defeated Mamelodi Sundowns in the final.
Pirates have now lost their last three cup finals:— Nkareng Matshe (@Nkareng) December 8, 2018
2016 Nedbank Cup v SSU
2017 Nedbank cup v SSU
2018 TKO v Baroka
Baroka are champs. More than four years without a trophy for Pirates - the heat is on.— Mazola J. Molefe (@superjourno) December 8, 2018
What a great cup final this was. Pity there had to be a loser. Congrats to @Baroka_FC for making history. Undoubtedly one of the best cup finals I've watched.— Nkareng Matshe (@Nkareng) December 8, 2018
CONGRATULATIONS | @Baroka_FC are the #TKO2018 CHAMPIONS after beating Orlando Pirates via penalties in the Final at the Nelson Mandela Bay Stadium!, They become the first team from Limpopo to win a Domestic Cup title in the PSL era. pic.twitter.com/sS8yQeCwxx— LimSportsZone (@LimSportsZone) December 8, 2018
Congratulations to @Baroka_FC for their TKO Final win! First time in a Cup Final ever & won! Massive congratulations! To both teams, Msanzi thanks you for one of the most thrilling Cup Finals we have witnessed #TelkomknockoutFinal #Champions pic.twitter.com/UiZMsS17HO— Golden Arrows FC (@goldenarrowsfc1) December 8, 2018