Josef Zinnbauer handed a first-team debut to Thabiso Sesane in defence, while Gabadinho Mhango was recalled after starting the last few matches on the bench.
Pirates posed all the first forays as a low free-kick towards the inside-left of the area from Deon Hotto 18 minutes in forced goalkeeper Xolani Ngcobo to parry for a corner-kick.
It was all Pirates closer to the break with Ben Motshwari firing a reverse pass from the near side by Mhango over the top before a low shot from Sipheshile Ndlovu brought a save off Ngcobo.
Uthongathi grew stronger as the first half flew by, with the Buccaneers unable to find a breakthrough despite seeing a lot of ball and offensive forays.
The Cane Cutters opened up the Buccaneers for the first time in the match early in the second half when a cutback from Nkosiyazi Maphumulo found Khetukuthula Ndlovu, who curled wide of the target.
However, the fears from the Pirates faithful died down three minutes later after Hotto brought down a ball over the top to play a low cross for Mhango to tap home comfortably.
Zinnbauer made three changes for Pirates minutes later as goalkeeper Siyabonga Mpontshane, Jean-Marc Makusu Mundele and Terrence Dzvukamanja were introduced.
Mpontshane was worked to his first save of the match with 15 minutes to go from a snap-shot on the turn from Tshepo Chaine with Innocent Maela heading wide from a corner at the other end.
Pirates got more openings late on, as Mundele dragged wide from close range before Thabang Monare rattled the upright with a thumping shot as it ended 1-0 to send the Soweto giants to the round of 16.
Pirates: Ofori, Hlatshwayo, Jele, Sesane, Maela, Monare, Motshwari, Ndlovu, Lorch, Hotto, Mhango.
Subs: Mpontshane, Mundele, Dzvukumajna, Tshobeni, Mntambo, Muwowo, Zungu, Dlamni, Makaringe.
Uthongathi: Ngcobo, Dlamini, Cele, Nxadi, Magawana, Slawula, Hlongwa, Maleka, Maphumulo, Ndlovu, Baloyi.
Subs: Amonome, Chaine, Lesoua, Ngcobo, Phiri, Silangwe, Zwane, Kunene, Shezi.