Goalkeeper Siyabonga Mpontshane started for the first time under Josef Zinnbauer, as Austin Muwowo, Kabelo Dlamini and a first start for Jean-Marc Mundele set out the rest of the side.
Mundele, who scored in the reverse fixture last Sunday in Gaborone, targeted back-to-back goals from a free-kick by Linda Mntambo on ten minutes but in the end fired against the side-netting.
Jwaneng became more resilient as the half entered the closing stages as a free-kick from range clattered the upright, leaving Mpontshane in sixes and sevens.
Pirates regained composure following the mini scare and nearly went to halftime in front through a close-range strike by Mntambo, but the latter slammed over the target.
Galaxy's stubbornness finally fell apart ten minutes in the second stanza when Mntambo picked up a ball inside the area to apply a composed finish past goalkeeper Ezekiel Morake.
Thabang Monare went close to doubling the lead before 60 minutes from a tee-up by Mundele, but the midfielder hoofed over the top from the edge of the area.
Pirates still enjoyed the better of the chances minutes later through a galloping run in the area by Muwowo, but Morake pulled off a stunning point-blank save.
Zinnbaeuer made a double substitution towards fulltime, as Monare made way for Nkanyiso Zungu before Thabiso Sesane entered for Hlatshwayo.
Nevertheless, tt was all Pirates in the closing stages with Zungu closing in from a free-kick and Bongani Sam a cross-cum shot from the left, as the Soweto giants secured their name in the hat for Monday's group stage draw.
Pirates: Mpontshane, Hlatshwayo, Maela, Nyauza, Sam, Mntambo, Monae, Tshobeni, Muwowo, Dlamini, Mundele
Subs: Sandilands, Sesane, Mako, Zungu, Makaringe, Makgaka, Ndlovu