In Group B, Coton Sport of Cameroon confirmed their semi-final berth by forcing a goalless draw away at Sewe Sport in Ivory Coast in the day's other match.
Coton Sport will finish second, behind Esperance of Tunisia who were confirmed group winners.
Esperance, runners-up last year and winners in 2011, had made sure of their progress to the final four on Saturday when Yannick Ndjeng scored an 81st minute winner in a 3-2 home win over Recreativo Libolo of Angola.
Egypt's Ahli came back after conceding an early goal in Sunday's match at El Gouna to effectively eliminate their compatriots from the competition. Ahli now need just one point to ensure top place in the final round of group matches next weekend.
Omar Gaber scored in the fourth minute for Zamalek, who needed victory to force a four-way tie at the top of the group, but their lead lasted only five minutes before Walid Soliman equalised and six minutes later Ahli were ahead through Ahmed Abdulzaher.
Ahli have 10 points, three more than AC Leopards of Congo and South Africa's Orlando Pirates. Leopards beat Pirates 1-0 in Dolisie on Saturday. Five-time winners Zamalek are on four points from their five group games.
Pirates host Ahli in their final group match on Sunday at the same time as Zamalek will play Leopards in El Gouna.