Mohamed Sherif scored his sixth goal of the competition after 53 minutes to put the Cairo Red Devils ahead at an empty Stade Mohammed V because of the coronavirus pandemic.
A brilliant goal from Mohamed 'Afsha' Magdy on 64 minutes left little doubt about the outcome in a disappointing finale to the marquee African club competition.
Amr el Sulaya rubbed salt into the wounds of Chiefs with a third goal on 74 minutes, slamming a back-heel past Nigerian goalkeeper Daniel Akpeyi.
Chiefs were struggling to contain Ahly late in the first half when they suffered a massive blow with the red-carding of Happy Mashiane.
The forward stamped on the right leg of full-back Ahmed Tawfik and, after initially flashing a yellow card, the Burundi referee checked the foul on a monitor and changed his decision.
It was a historic victory for Ahly, who became the first club to win back-to-back Champions League titles three times.
South Africa-born Ahly coach Pitso Mosimane, who supported Chiefs as a child, became the first African coach to win the competition three times.
He succeeded in 2016 with South African club Mamelodi Sundowns, and again with Ahly last season in an all-Egyptian final against fierce rivals Zamalek.
Before travelling to the Far East, the Egyptian club that have won 22 African titles will play CAF Confederation Cup winners Raja Casablanca of Morocco in a one-off match for the CAF Super Cup.