The Buccaneers recalled Thembinkosi Lorch from the onset after he came off the bench in last Sunday's first-leg in Soweto and also started Thabang Monare in midfield, while there was recognised strike in the line-up.
Pirates should've been in the lead following six minutes from a clear chance by Siphesihle Ndlovu off a ball in behind by Deon Hotto, but he was unable to beat the opposite number.
That missed opportunity didn't go unpunished as two minutes later Ben Malango headed home a delivery from Omar Arjoune with the defence caught unaware.
The Green Eagles doubled their lead midway in the first half through a well-taken first-time strike in the area by Zakaria El Wardi following a cutback from Soufiane Rahimi.
Pirates were cut into pieces following the half-hour mark as Rahimi picked up a loose ball misplaced set-piece by the visitors to run in on goal before going over goalkeeper Wayne Sandilands.
More woes followed for Bucs as the Green Eagles made it four ten minutes to halftime with a smartly taken finish from Malango with Rahimi the supplier yet again.
The one-sided first half led the Buccaneers to a double substitution in Nkanyiso Zungu and Gabadinho Mhango ahead of the second half.
Mhango immediately tested the home side with a header from a set-play delivery, but he could only draw a save from goalkeeper Anas Zniti.
Pirates pushed more bodies forward as the half went on and Mhango was on the end of another opportunity from a free-kick, but Malango cleared.
The Green Eagles weathered the storm to progress to the last four with a comprehensive 5-1 aggregate victory.
Pirates: Sandilands, Hlatshwayo, Maela, Jooste, Mako, Ndlovu, Mabaso, Monare, Pule, Hotto, Lorch
Subs: Ofori, Motshwari, Zungu, Mntambo, Makaringe, Dlamini, Sam, Nyauza, Mhango