The Buccaneers played the last 30 minutes of the match with 10 men, as Senzo Meyiwa was sent off, but Happy Jele's goal early in the second half proved to be enough to hand them a victory over Ea Lla Koto.
Pirates join Black Leopards, Mpumalanga Black Aces and Baroka FC in the semi-finals.
Thulasizwe Mbuyane made a return from injury, however Bucs were without left-back Reuben Cloete.
Lucky Lekgwathi filled in on the left, but struggled and committed a few errors.
After a scrappy opening, Pirates came to life around the midway point of the first half.
Francis Chansa and Jele both tried their hand at long-range efforts that were easily saved by Kennedy Mweene, while Chiukepo Msowoya had a penalty appeal turned down by referee Victor Hlungwani.
Stars’ Noah Chivuta came close to breaking the deadlock in the 28th minute with a cheeky chip from long range that carried just over Senzo Meyiwa’s crossbar and brushed the top of the netting.
On 36 minutes Bucs created the best chance of the first half, with a ball over the top sending Thulasizwe Mbuyane free down the left of the penalty area.
But Mbuyane scuffed a low shot wide of the mark when a square pass for Chansa would have been a tap-in.
Just before the break Pirates twice tested Mweene through Msowoya and Mbuyane; the latter effort was a stinging turn-and-volley that forced the Ea Lla Koto goalie into an acrobatic save.
Bucs’ perseverance was rewarded nine minutes after the restart when Jele continued his great form by putting the hosts 1-0 up.
A 54th-minute Dikgang Mabalane corner-kick was cleared straight back to 'Terminator', whose second cross to the near post was glanced home by the unmarked Jele.
Pirates seemed to be in the driving seat, but just past the hour mark Noah Chivuta slipped through on goal and Meyiwa sprinted off his line, tripping him up just outside the penalty area.
Referee Hlungwani had no choice but to show a red card to the keeper, who had denied a clear goalscoring opportunity.
Bucs brought on third-choice goalkeeper Jacob Mokhasi, sacrificing Msowoya up-front.
The new man between the posts made a terrific last-gasp save in the 74th minute, somehow denying Madoda Motha when he looked certain to force the ball over the goal-line from close range.
Stars, with a man’s advantage, dominated possession in the latter stages, though it was Pirates, through the pace of Mabalane and substitute Tlou Segolela, that actually looked the likelier scorers.