Despite playing with ten men from the 55th minute onwards after defender Mahmoud Rezk was sent off for misconduct, the hosts managed to overcome their 1-0 first-leg defeat in Tanzania two weeks earlier.
Striker Ahmed Atef opened the scoring early on, giving the Egyptian representatives a seemingly comfortable advantage.
However, Marouf Tchakei silenced the home crowd in the 28th minute, leveling the score.
With the visitors' goal, Modern Future FC became desperate to score a couple of goals to secure their qualification for the next round.
Winger Ahmed Refaat added the second just eight minutes after the break, but defender Mahmoud Rezk made the hosts' mission more challenging by receiving a direct red card right after the goal.
International fullback Omar Kamal extended the lead to 3-1 with a solo effort in the 68th minute.
Despite the visitors’ pressure in search of a crucial qualification goal, a late strike from the playmaker Nasser Maher in injury time sealed the victory and put the game out of reach.
Modern Future FC will now join fellow Egyptian club Zamalek in the Group stage, who secured their qualification on Saturday at the expense of Arta Solar from Djibouti.
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