Zamalek booked their spot in the semi-finals, despite losing 1-0 to ES Tunis in the quarter-final second-leg at Stade Olympique de Rades.
Billel Bensaha gave Esperance an early lead in the fifth minute from the penalty spot but that proved to be the only goal of the match, as Zamalek held on to a 3-2 aggregate victory, after winning the first-leg 3-1.
The Egyptian side will be up against Moroccan outfit Raja Casablanca in the semi-finals in May.
Raja Casablanca are through to the semi-finals despite a 1-0 loss against TP Mazembe in the second-leg at Stade Frederic Kibassa Maliba.
After a goalless first stanza, Isaac Tshibangu finally broke the deadlock for Mazembe five minutes into the second stanza.
The Congolese side had a glorious chance to make it 2-0 after they were awarded a penalty with 19 minutes left but Jackson Muleka missed the spot-kick.
Raja, after winning the first-leg 2-0 on home soil, went through with a 2-1 aggregate win and will come up against Zamalek in the semi-finals in May.
Wydad Casablanca are throught to the semi-finals with a 2-1 aggregate victory over Etoile du Sahel in the quarter-final second-leg at Stade Olympique de Rades.
Karim Aribi broke the deadlock for Etoile just before the hour-mark but the Tunisian side could not get the second goal to force the match to extra-time after losing the first-leg 2-0.
Wydad held on in the end and will face Egyptian giants Al Ahly in the semi-finals in May.