The match had finished 1-1 after 90 minutes, with the Buccaneers dominating the first half and scoring through Sifiso Myeni.
However, Amakhosi fought back strongly after the the break and equalised through Reneilwe Letsholonyane.
Pirates have hardly had an off-season given their CAF Confederation Cup commitments, and it showed in the opening exchanges as they were much sharper and quicker to the ball than Chiefs.
The first chance came in the eighth minute, when Myeni showed great skill down the left to skin Kgotso Moleko and cross to an unmarked Thamsanqa Gabuza, only for Siyanda Xulu to get a toe on the ball and clear the danger.
Reyaad Pieterse, a late replacement for Brilliant Khuzwayo, had to be at his best in the 17th minute to keep out Gabuza’s low drive, before pulling off and even better save a minute later to parry Thabo Rakhale’s long-range curler.
However, there was nothing the goalkeeper could do on 20 minutes as Myeni opened the scoring with a pinpoint free-kick.
The goal seemed to wake Chiefs up as they steadily found their feet and gave Brighton Mhlongo something to think about.
Letsholonyane blasted over from the edge of the area on 34 minutes, before substitute Tendai Ndoro was forced to clear off the line after Mhlongo had spilt a high-ball.
Chiefs’ best chance of the half came just before the break when George Lebese swung a perfect cross into David Zulu right in front of goal, but rather than hit it first time, the striker opted to take a touch and the moment was lost.
The second half started with a flurry of chances, the first of which fell to Siphiwe Tshabalala straight after the restart. Bernard Parker found him at the back-post with a pin-point cross, but ‘Shabba’ headed wide.
Lehlohonolo Majoro skewed a shot wide from inside the area shortly afterwards, before the fans made their substitutions: Willard Katsande coming on for George Maluleka and Mansi Masuku replacing ‘Major’.
Ndoro was making his presence felt on ‘debut’, and stung Pieterse’s palms with a powerful drive on 58 minutes, before Mhlongo acrobatically tipped over Shabba’s free-kick.
Steve Komphela brought on Siphelele Mthembu just past the hour-mark, and his first touch was a beautiful flick-on to Yeye, who burst into the box and slotted past Mhlongo to level the scores.
Masuku and another ‘debutant’, Luvoyo Memela, went close for Pirates towards the end, but ultimately the match would be decided by penalties.
Patrick Phungwayo missed for Pirates, but Mhlongo twice saved from Keegan Ritchie and Letsholonyane as Bucs beat their archrivals on penalties again.