Linda Mntambo came in for the injured Thembinkosi Lorch as Pirates' only change from the 1-1 draw with SuperSport United this week, while Cameron Carnell was handed his first for the Team of Choice.
Maritzburg broke the deadlock in the opening eight minutes when Thabiso Kutumela got on the end of Richard Ofori's error outside the box to slot into an empty net.
The Buccaneers looked for a quick reply through a cutback from the left-side by Fortune Makaringe, but Mntambo tapped narrowly wide from a promising position in the six-yard area.
An early change on the side of Maritzburg saw Kwanda Mngonyama withdrawn through injury as Phiwayinkosi Zuma was drafted into the field of play.
This didn’t seem to bother the Team of Choice who nearly had a second goal with a looping header in the area from Lungelo Bhengu, but goalkeeper Ofori tipped over the crossbar.
Josef Zinnbauer revived his stall ahead of the second half, as Ben Motshwari made way for Kabelo Dlamini. As a result, Pirates drew level ten minutes from resumption when a first-time shot outside the area by Dlamini deflected past goalkeeper Marcel Engelhardt.
A second came within a minute after Deon Hotto met a low cross from the right-side to slide in at the back-post with Engelhardt in no man’s land.
Pirates were denied a third soon thereafter as a well-taken free-kick from outside the area by Vincent Pule crashed against the side-netting.
Pule weren’t prohibited again with 12 minutes to go as he reacted first to a loose ball from a spill by Engelhardt to riffle in from the near side.
The Buccaneers controlled the closing phases of the match to secure the come-from-behind victory and a quarter-final spot in the process.