Zamalek conceded two late goals at CotonTchad in N'Djamena but sealed smooth progress to the African Confederation Cup third round with a 7-2 aggregate win on Saturday.
Despite their comprehensive 7-0 first-leg win, Zamalek coach Christian Gross opted to field an almost full-strength side in a dour affair played on an artificial pitch.
The White Knights wasted several goal-scoring chances, especially in the second half.
Winger Mahmoud Kahraba missed a sitter from close range and left-back Abdallah Gomaa failed to beat the keeper in a one-on-one with five minutes remaining.
CotonTchad scored two goals in the dying stages for a morale-boosting win for the hosts.
Abanga youssouf volleyed home from inside the area and they scored again in stoppage time.
Zamalek are now the only Egyptian representative left in Africa's secondary club competition after Masry were eliminated following a 2-0 aggregate defeat by Burkina Faso's Salitas on Saturday.
Ahly, Zamalek's Cairo rivals, are the only Egyptian side to win the Confederation Cup, having lifted the trophy in 2014.
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