Sundowns edged Zamalek of Egypt 1-0 in a cagey Pretoria clash after Ali Gabr conceded an own goal 11 minutes from time on a cold southern hemisphere winter night.
Colombian Leonardo Castro should have given Sundowns an early lead, but blazed over with a clear sight of goal, and El Shenawy used a leg to foil Zimbabwean Khama Billiat later in the half.
The South Africans have nine points from three victories in Group B, a mini-league reduced to three clubs when Entente Setif of Algeria were kicked out over a pitch invasion.
Five-time African champions Zamalek have three points having won only one of three matches and two-time champions Enyimba of Nigeria are pointless following two losses.
Zamalek will join Sundowns in the semi-finals if they do not lose at home to Enyimba during August.
Reaching the semi-finals continues a remarkable turnaround for Pretoria outfit Sundowns after they were eliminated in the final qualifying round only to be reinstated.
On the eve of the group draw it was discovered that V Club of the Democratic Republic of Congo, who beat Sundowns, had fielded an ineligible player and they were disqualified.
Rami Rabia scored in the first minute of the second half to give Ahly a surprise 1-0 away win over Group A leaders Wydad Casablanca of Morocco in Rabat.
The defender darted forward to nod a free-kick wide of goalkeeper Zouheir Laaroubi and into the corner of the net.
It was a must-win match for Ahly after collecting just one point from a possible nine in three previous mini-league matches.
The result sets up an intriguing climax during August with Wydad and Zesco United of Zambia having seven points each and ASEC Mimosas of the Ivory Coast and Ahly four apiece.
Zesco came from behind to draw 1-1 with ASEC in a lacklustre Abidjan match.
Nabi Kone nodded the hosts ahead in the second half and Jackson Mwanza levelled three minutes later.
The seven title contenders are chasing a $1.5 million (1.35 million euros) first prize and a place in the 2016 FIFA Club World Cup in Japan.