Zanaco did just enough to earn a place in the quarter-finals after a 1-1 draw with RSB Berkane at Stade Municipal de Berkane.
Alain Traore grabbed the lead for Morrocan side in the second minute but an own goal by Issoufou Dayo six minutes before the break gave Zanaco a lifeline, as the sides shared the spoils in the end.
Berkane qualified as Group B winners while Zanaco settled for a second position with ten points.
Enugu Rangers and El Masry ended their Group A campaign with a 1-1 drawat Nnamdi Azikiwe Stadium on Sunday
Rangers' Ifeanyi George cancelled out Mahmoud Wadi's early for El Masry in the 20th minute, as the sides shared the spoils.
El Masry were already through to the quarter-finals and finished as runners-up with ten points while Rangers finished third.
Motema Pembe missed out on the quarter-final place despite beating FC Esae 1-0 in the last match of Group B at Stade des Martyrs.
Vinny Kombe scored the only goal of the tie for the Congolese side in the third minute but victory was not enough to earn a place in the next round, as they finished third, tied on points with second-placed Zanaco, who boasted the better head-to-head record.
Horoya finished six points clear at the top of Group C after beating Al-Nasr 2-0 at Martyrs of February Stadium.
Boniface Haba got the opener in the 11th minute before Dramane Nikiema sealed the three points 14 minutes before time.
Al-Nasr were already through to the quarter-finals, with their second place secure despite being level on eight points with third-placed Djoliba.
Egyptian side Pyramids FC finished at the top of Group A after edging Nouadhibou 1-0 at 30 June Air Defence Stadium.
After a goalless first stanza, Ahmed Mansour eventually broke the deadlock for Pyramids just before the hour-mark and that proved to be the winner.
Paradou missed out on a place to the quarter-finals despite thrashing Hassania Agadir 3-0 at Stade Adrar.
Oussama Kismoun netted a brace while Yousri Bouzok added the third goal in stoppage time for the Algerian side.
HUSA qualified for the quarter-finals, as they finished top of Group D with points while Paradou ended up in third place, two points behind Enyimba, who also booked a last eight spot after thumping San-Pedro.
Nigerian giants Enyimba booked their spot in the quarter-finals after thumping San Pedro 5-2 in the final match of Group D at Stade Felix Houphouet-Boigny in Abidjan.
Victor Mbaoma netted a brace while Abdulrahman Bashir, Augustine Oladapo and Stanley Dimgba were also on target for Enymba.
Sherif Jimoh and Irie Zan Bi scored for San Pedro but it was not enough as they finished at the bottom of the group.
Pyramids FC
Al Masry
Horoya AC
Al-Nasr
RS Berkane
Zanaco
Hassania Agadir
Enyimba