TP Mazembe secured top spot in Group A with a 3-1 win over Zesco United at the Stade TP Mazembe on Saturday.
A double from Jacob Muleka either side of the half led Mazembe on their way, with Chico Kubanza netting a third.
Zesco's consolation came in the 34th minute through Winston Kalengo, as the Zambians exit the tournament without a win in the group.
Group A's other encounter between Primero de Agosto and Zamalek at the Estadio 11 de Novembro in Luanda finished goalless.
Zamalek joins Mazembe in the quarter-finals after gathering nine points and two wins in their group stage journey with Agosto eliminated.
USM Alger and Petro de Luanda played to an entertaining 2-2 draw at the Stade du 20 Aout 1955 in Group C.
USM went into the break leading through Aymen Mahious before Oualid Ardji doubled their lead in the second half.
Petro replied in the last ten minutes and found their just rewards through Domingos Sengui and Toni.
Reigning champions Esperance suffered their first defeat after going down 1-0 to JS Kabyile in a Group D clash.
The only goal of the match arrived on 56 minutes through Rezki Hamroune, as JS finished the campaign third in the group while Esperance finish top of the table.
Raja Casablanca joined Esperance in the knockout stages with a 1-0 victory at the Stade Mohammed V in Casablanca.
A third-minute strike from defender Badr Banoun separated the two sides, with the visitors eliminated from the tournament.
Al Ahly failed to secure top spot in Group B following a 1-1 draw against Sudan's Al-Hilal at the Al-Hilal Stadium.
Mohamed Magdy provided the game's opening goal after 48 minutes, but Hilal levelled in added time to through Abdelrazig Omer.
Etoile du Sahel maintained top spot in Group B after securing a 2-0 victory over Zimbabwe's FC Platinum in Rades.
Karim Aribi put the hosts ahead after after halftime before Malek Baayou sealed the match minutes before full-time.
Mamelodi Sundowns
Al Alhy
Zamalek
TP Mazembe
ES Tunis
Raja Casablanca
Wydad Casablanca
Etoile de Sahel