After a first half of few chances, the Chinese champions took the lead in the 49th minute when Brazilian Elkeson converted from close range after Muriqui had seen his effort cleared off the line.
Dario Conca doubled their lead midway through the second half, timing his run perfectly to convert from 12 yards after goalkeeper Sherif Ekramy had denied Muriqui.
The victory is Guangzhou's 39th of 2013 and will see Marcello Lippi's AFC Champions League winners face the UEFA holders in the last four of the competition.
Both sides named attacking line-ups with Muriqui - who scored 13 goals in continental action this season – leading the line for Guangzhou, while Mohamed Aboutrika started in support of Emad Moteab for Al Ahly.
The Egyptians started more quickly than their opponents and should have scored in the sixth minute, but Aboutrika wasted the chance as he headed over the crossbar from six yards.
That let-off sparked Guangzhou into life and after working their way back into the game, they should have opened the scoring nine minutes later.
Zheng Zhi did well on the left before rolling the ball into Elkeson, the Brazilian striker racing past his marker before dragging his shot just wide of Ekramy's left-hand post.
Neither side came close to scoring before the break but four minutes into the second half Elkeson gave Guangzhou the lead.
Muriqui broke through the Al Ahly defence to meet a throughball and when his effort was blocked by Ahmed Fathy and diverted onto the post, Elkeson had the simple task of converting from two yards.
Two minutes later, Muriqui had chance to double Guangzhou's lead when he again evaded the Al Ahly defence only to volley wide.
Mohamed Youssef's side began to pose a threat from set-pieces and Rami Rabia should have equalised from a corner.
The midfielder got ahead of his marker at the front post but his flicked header did not test goalkeeper Zeng Cheng as it looped over the crossbar.
Conca booked Guangzhou's place in the semi-finals in the 67th minute - Muriqui again racing away from the Al Ahly defence before his shot was well saved. Conca arrived in time to stroke the loose ball into the back of the net.
Lippi's side will now remain in Agadir after their victory as they now meet Munich in the last four at the same ground on Tuesday.