A goal from Peter Shalulile midway through the first half helped Sundowns complete the double over the reigning African champions, having stunned them in Cairo with the same 1-0 victory last month.
Ahly looked worn out due to a packed schedule, with the team having played their third match in less than a week. They were largely outplayed at the Soccer City Stadium in Johannesburg as Sundowns controlled proceedings.
The visitors struggled to string passes together and frequently gave away possession in their own half. They were indebted to goalkeeper Mohamed El-Shennawi for keeping them in the game with a couple of superb stops in the second half.
Sundowns top the group with 10 points, six ahead of Ahly and Sudanese duo Al-Merreikh and Al-Hilal in an exciting three-horse race for the second group ticket to the last eight.
Despite the defeat, Ahly still have destiny in their own hands as they will host Al-Merreikh and Al-Hilal in Cairo in their final two games.
Ahly were guilty of too many mis-placed passes in the first half, with Sundowns closing them down and launching some swift moves upfront.
Despite playing with a midfield comprising of three defensive-minded players, Ahly found it hard to contain Sundowns' free-flowing football.
Sundowns went close on 22 minutes when a deflected shot from Mothobi Mvala struck the bar but they made amends from the resulting corner.
Lyle Lakay whipped in a cross from the left and Shalulile popped up unmarked at the far post to knee the ball home from close range.
Ahly had their first sight of goal on 36 minutes when an angled shot from Tunisian left-back Ali Maaloul went over the crossbar.
Sundowns remained in control in the second half, with Ahly offering no response.
Haashim Domingo could have doubled their lead three minutes past the hour mark when he created space for himself in the area after a pull-back from Shalulile, only for El-Shennawi to smother his low shot at his near post.
The Egypt keeper came to Ahly's rescue with an even better save 10 minutes later, thwarting substitute Pavol Safranko in a one-on-one following a defence-splitting pass and a recurring mistake from midfielder Amr El-Sulaya.
Ahly could have still snatched an equaliser late on but substitute Hossam Hassan sent a free header wide when he was picked out unmarked by an inviting cross from Maaloul.
(For more sports news and updates, follow Ahram Online Sports on Twitter at @AO_Sports and on Facebook at AhramOnlineSports.)