Tendai Ndoro was the hero for the Buccaneers, netting two second half goals to send his team through to the last 16 draw.
Chiefs were not without their chances, but Pirates were more clinical in the final third and were rewarded with a spot in the next round.
Bucs started like a house on fire, dominating Chiefs in the early exchanges and creating a number of chances.
Ndoro showed blistering pace as he outstripped the defence down the left, but Reyaad Pieterse did well to save his powerful shot from a tight angle.
Thabo Rakhale shot over shortly afterwards, before Gift Motupa squandered the best chance of the half, somehow managing to miss the target from three yards out.
Chiefs gradually started working their way back into the area, with the unmarked Camaldine Abraw just failing to reach Siphiwe Tshabalala's cross, before the striker failed to connect with Bernard Parker's cutback on the half-hour mark.
Brighton Mhlongo then saved Shabba's curling effort, before Amakhosi squandered their best effort of the half - Parker volleying inches wide from the edge of area.
Tshabalala missed a good chance shortly after the break when the ball got stuck under his feet inside the box, and another chance was wasted on 71 minutes when Chiefs broke 3-on-2 but, rather than pass, George Maluleka opted to go it alone and the moment was lost.
Parker then fired wide before the opening goal of the game came on 77 minutes. Mpho Makola played a lovely chipped pass to Ndoro, whose first touch was brilliant and his turn and shot even better.
Chiefs would have levelled five minutes later when Shabba looked to fire home from close range, but for Thabo Qalinge's brilliant tackle tracking back.
And that proved the difference as Pirates went up to the other end and got a second through Ndoro - his long-range shot slipping through Pieterse's fingers and into the back of the net.
The Zimbabwean almost completed a hat-trick in injury-time, but his curling effort on the turn missed by inches.
