Nigerian minnows Heartland followed in the footsteps of their local rivals Kano Pillars, who stunned Ahli with a 2-2 away draw, which favored the former.
Coton, who were beaten 4-2 on aggregate by Ahli in last year's final, will now play in the CAF Confederation Cup, along with the Egyptian giants.
Elsewhere, Sudanese champions Merreikh drew 1-1 at home with Uganda's Kampala City, but went through to the Champions League group stage with a 2-1 aggregate win.
Etoile Sahel of Tunisia beat Ahli Tripoli 2-0 in Sousse to qualify with the same aggregate score, following a goalless first-leg draw.
Morocco's Ittihad Khemisset were held to a 0-0 home draw by Mazembe of DR Congo, who won 1-0 on aggregate.
Zesco United of Zambia edged Mali's Djoliba 2-1 to qualify for the quarter-finals as well.
The two remaining slots for the last eight phase will be decided on Sunday, when Monomotapa United host ASEC Mimosas in Zimbabwe and Desportivo of Angola visit Sudan's Hilal.