The Egyptian side trailed 2-1 from the first leg and Sewe Sport appeared set to become the first Ivorian club to lift the cup since its inception in 2004.
That is until Emad Moteab's header in the sixth minute of stoppage time sent the majority of the Cairo International Stadium crowd wild as Al Ahly triumphed on the away goals rule.
Al Ahly are one of Africa's most successful clubs having won the continent's Champions League eight times.
The Egyptian outfit dropped into the CAF Confederations Cup this season, however, after being knocked out of the top-tier competition.
Sewe Sport looked like inflicting another defeat on them in Saturday's second leg as the visitors carved out all the early chances.
Souleymane Dembele hit the crossbar in the first half with a powerful effort, but as the finish line came into view, the Ivorian outfit dropped deeper towards their own goal.
That invited increasing levels of pressure from Al Ahly, and Moussa Yedan had an effort cleared off the line early in the second half as the hosts pushed forward.
Al Ahly eventually made the breakthrough when Moteab found space in the box to meet Walid Soliman's right-wing cross with the header that underlined the value of Trezeguet's away goal in Abidjan.
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