There was little to play for in the second half after the hosts turned on a dominant display in the first half to race to a healthy lead.
It meant a subdued Pirates needed to score four goals in the second half to level terms and book a spot in the semi-final.
But the experienced Moroccans calmly managed the game in the second half, knowing a last four spot was all but secured.
The introduction of Gabadinho Mhango, last season’s joint top scorer with 16 goals, early in the second half seemed a little too late.
Pirates had the first chance of the game in the sixth minute when Deon Hotto played Siphesihle Ndlovu in, but the former Maritzburg United midfielder’s shot was blocked by the keeper Anas Zniti.
They were duly punished two minutes later when Raja took the lead through Ben Malango, who headed in for the opener after a perfect delivery from Omar Arjoune.
The Congolese forward was the scorer of the solitary goal at Orlando Stadium last Sunday.
Bucs had the chance to draw level in the 15th minute when Vincent Pule set up Hotto, but Raja’s keeper Zniti was equal to the task, making another vital block in a one-on-one situation.
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.
At the half-hour mark, Rahimi, who is linked to Pitso Mosimane’s Al Ahly, added the third. He picked up a loose ball and raced towards goal under challenge before looping it over veteran goalkeeper Wayne Sandilands.
Malango got his second of the day and the fourth for the Green Eagles ten minutes before the break with a smartly taken finish after Rahimi set him up.
After keeping Bucs’ attackers at bay in the second half, Raja are through to the semi-final of the Caf Confederation Cup.
By Mthokozisi Dube