In the semi-finals, the South Africans will face Wydad Casablanca of Morocco and defending champions Esperance of Tunisia meet TP Mazembe from the Democratic Republic of Congo.
Sundowns built an unexpectedly big 5-0 first-leg lead last weekend, leaving heavily-decorated Ahly needing to stage the greatest comeback in the 55-year competition to survive.
When the Egyptian side failed to score in the first half at the Borg el Arab Stadium near ancient Mediterranean city Alexandria, the writing was on the wall.
The record eight-time Champions League winners finally broke down the resilient Sundowns defence on 68 minutes when Walid Azaro nodded an Ahmed Fathy cross past Denis Onyango.
But that was as good as it got for the hosts, who have won an unprecedented 19 CAF competitions, eight more than Mazembe.
Ugandan Onyango starred for Sundowns, making a string of brave saves, especially in the second half when Ahly laid siege to his goalmouth.
It was third time lucky for Sundowns against Ahly after losing to them in the 2001 final and a 2007 qualifier.
The Pretoria outfit won the Champions League in 2016 and the margin of victory will raise hopes that they can become the first South African club to lift the trophy twice.
Losing by four goals on aggregate equalled the worst performance by Ahly in Africa -- a 4-0 overall defeat to Enugu Rangers of Nigeria 16 years ago in the now defunct CAF Cup.
Mazembe overcome early scare
Meanwhile, Mazembe recovered from conceding a 90-second goal to trounce Simba SC of Tanzania 4-1 in Lubumbashi after a goalless first leg last Saturday.
Ugandan Emmanuel Okwi silenced the capacity 20,000 in the southern Congolese mining city by darting on to a through ball and rounding the goalkeeper before tapping into the net.
Mazembe, whose last of five Champions League titles came in 2015, recovered to lead 2-1 at half-time through goals from Zambian Kabaso Chongo and Elia Meschak.
Chongo poked the ball into the net after a goalmouth scramble while Meschak used his renowned dribbling skills to put his team ahead.
A parry by Simba goalkeeper Aishi Manula on 62 minutes gave veteran Tresor Mputu the chance to make it 3-1 and Jackson Muleka completed the rout 15 minutes from time.
Mputu and Muleka have scored five goals each in the Champions League this season, two less than long-time chart-topper Moataz al Mehdi from already eliminated Al Nasr of Libya.
Wydad and Esperance comfortably advanced to the last four having achieved good away results last weekend.
The Moroccans overwhelmed Horoya AC of Guinea 5-0 in Rabat after a goalless first leg with Walid el Karti scoring twice within 10 minutes during the first half to trigger the rout.
Mohamed Nahiri netted in the second half to raise his CAF goal tally for the season to five, an excellent achievement for a left-back.
Esperance completed a double over CS Constantine of Algeria, following up an away victory by winning 3-1 in Rades near Tunis for a 6-3 overall triumph.
Saad Bguir, whose two goals against Ahly won Esperance the 2018 final, scored twice in four minutes during the first half to ensure there would be no dramatic Constantine comeback.