Wayne Sandilands returned in goal for the Buccaneers along with Ntsikelelo Nyauza and Paseka Mako in defence, while Vincent Pule and Linda Mntambo also earned re-calls.
Augustine Mulenga inched closer to the breakthrough with a powerful drive on 17 minutes, but Lee Langeveldt acrobatically palmed the effort for a corner.
Stellies remained edged on the cusp of the box, as the Buccaneers aimed to unlock the defensive block with balls to the wide areas.
Pirates missed an absolute sitter on 25 minutes as Mulenga powered against the crossbar, while Pule went against the side-netting from a free-kick seconds later.
The Buccaneers continued firing blanks in the later stages, with Tshegofatso Mabasa lobbing over the top after going toe-to-toe with Langeveldt.
Stellies brought more stability to their approach with a double change 12 minutes into the second half, as Leletu Skelm and Robyn Johannes entered the party.
Langeveldt continued to frustrate Pirates with quick-fire saves moments after each other, tipping over the bar from Thembinkosi Lorch and denying Mako in the matter of minutes.
Mulenga’s evening though ended in the 65th minute as Rhulani Mokwena went for a different approach with the arrival of Justin Shonga.
However, the Buccaneers went in front in the final seven minutes when Lorch picked a pass from Makaringe to blast into the bottom corner.
Langeveldt denied the Sea Robbers a second with strong saves in the final minutes following shots from Lorch and Mabasa, but one goal was enough to seal their spot in the next round alongside Maritzburg United, Golden Arrows and Kaizer Chiefs.
Pirates: Sandilands, Jele, Nyauza, Mako, Monyane, Mntambo, Makaringe, Lorch, Pule, Mulenga, Mabasa.
Subs: Delle, Ndengane, Mlambo, Ndlovu, Memela, Dlamini, Shonga
Stellenbosch: Langeveldt, Bergman, Ndlovu, Robertson, De Goede, Mobbie, Zungu, Motsogi, Rayners, Van Rooyen, Afoakwa.