Victor Mbaoma scored twice as former African champions Enyimba trounced San Pedro of the Ivory Coast 5-2 in Abidjan to fill the second qualifying place in Group D.
Zanaco came from behind to force a 1-1 at Renaissance Berkane of Morocco, who had scored 13 unanswered goals in four previous CAF home matches, and finish Group B runners-up.
Pyramids and Al Masry of Egypt, Berkane and Hassania Agadir of Morocco, Horoya of Guinea and Al Nasr of Libya had secured knockout places before the final matchday.
The draws for the quarter-finals and semi-finals in the African equivalent of the UEFA Europa League will be made in Cairo this Wednesday with group winners and runners-up kept apart.
Abdulrahman Bashir and Mbaoma netted for Enyimba within three minutes of the kick-off and the 2003 and 2004 CAF Champions League winners led 3-2 at half-time.
In the closing stages, Mbaoma and Stanley Dimgba each scored their fourth goal of the Confederation Cup season to seal an impressive victory.
Enyimba, the most successful Nigerian club in CAF competitions with four titles, had scored only six goals in five previous group matches.
Agadir won the group, finishing one point above Enyimba despite a shock 3-0 home loss to third-place Paradou of Algeria.
Meanwhile, Zanaco needed a draw in northeastern Moroccan city Berkane to be sure of retaining second place and qualifying for the knockout stage.
– Began disastrously –
The bank club from Lusaka began disastrously, conceding a goal within two minutes as Burkinabe Alain Traore scored for Berkane, runners-up to Zamalek of Egypt last season.
However, the Zambians gradually regained their composure and levelled before half-time when Rodgers Kola scored his sixth goal of the Confederation Cup campaign.
Zanaco then survived a second-half pummeling from Renaissance to finish ahead of Daring Club Motema Pembe of the Democratic Republic of Congo.
After taking a third-minute lead through Vinny Kombe, Motema Pembe failed to score again against bottom-of-the-table ESAE of Benin and had to settle for a 1-0 win in Kinshasa.
But it proved a hollow victory as the Congolese outfit were eliminated on head-to-head records having drawn at home and lost away to Zanaco.
Hopes that already eliminated Enugu Rangers of Nigeria could finish on a high note proved unfounded as they were held 1-1 at home by Group A runners-up Masry.
Palestinian international Mahmoud Wadi gave the Port Said club an early lead that Ifeanyi George cancelled midway through the first half.
A disastrous campaign for South African club Bidvest Wits ended with a 2-0 defeat by Djoliba of Mali in Soweto, which condemned them to last place in Group C.
