Sundowns made just one change from the first-leg defeat in Cairo, with Anele Ngcongca coming in for Wayne Arendse in defence.
Themba Zwane got a chance to bring Sundowns back in the overall contest after just two minutes from kickoff, but went over the top from range.
A quickly taken free-kick from Gaston Sirino two minutes later found the oncoming Ricardo Nascimento, who had his effort smothered by Mohamed El Shenawy.
Ahly stretched their overall advantage in the tie after Lebohang Maboe turned Ali Maaloul's free-kick into his own net 21 minutes in to make 1-0 in the second leg and 3-0 on aggregae.
Sirino, however, brought the home side level four minutes later with a simple tap-in after Zwane had his initial effort palmed by El-Shenawy.
Masandawana looked for a second just after the half-hour mark, but Sibusiso Vilakazi's header off Hlompho Kekana's cross went straight to El-Shenawy.
Sundowns coach Pitso Mosimane went on the charge straight after halftime with the introduction of Tebogo Langerman coming in Mosa Lebusa at the back.
Maboe looked to atone for his own goal at the other end with a close-range volley from Langerman's ball on 52 minutes, but the attempt flew over the top.
Sundowns had the Red Devils pinned into their own half towards the final quarter with Zwane's thumping strike forcing El-Shenawy to pull off an equally good save.
Denis Onyango was called into action later on as the Ugandan shot-stopper smothered Junior Ajayi's dangerously looking strike behind.
Good work from Vilakazi looked to pick out Jose Ali Meza for the winner with a cross in the latter stages of the second half, but El-Shenawy collected the danger to see his side into the semi-finals.
Sundowns: Onyango, Madisha, Nascimento, Lebusa, Ngcongca, Kekana, Jali, Sirino, Zwane, Vilakazi, Maboe.
Subs: Mweene, Langerman, Arendse, Mabunda, Mahlambi, Mhulise, Meza.
Al Ahly: ElShenawy, Maaloul, Rabia, Yaser, Fathy, El Soulia, Dieng, Metwally, Geraldo, Ajaye, Badji.