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| 1st(1st leg) | Kampala City Council FC | - | SuperSport United | 2:1 | ||
| 2nd (2nd leg) | SuperSport United | - | Kampala City Council FC | 1:1 | ||
| 1st(1st leg): 13/03/2009 13:00 | 2nd (2nd leg): 04/04/2009 19:00 | Winner: Kampala City Council FC | ||||
| 1st(1st leg) | Al Ittihad Tripolis | - | Al Merrikh SC | 1:1 | ||
| 2nd (2nd leg) | Al Merrikh SC | - | Al Ittihad Tripolis | 3:0 | ||
| 1st(1st leg): 13/03/2009 15:30 | 2nd (2nd leg): 04/04/2009 18:00 | Winner: Al Merrikh SC | ||||
| 1st(1st leg) | AS Douanes | - | Kano Pillars | 1:1 | ||
| 2nd (2nd leg) | Kano Pillars | - | AS Douanes | 0:0 | ||
| 1st(1st leg): 14/03/2009 | 2nd (2nd leg): 04/04/2009 | Winner: Kano Pillars | ||||
| 1st(1st leg) | Ajax Cape Town | - | Monomotapa United | 3:2 | ||
| 2nd (2nd leg) | Monomotapa United | - | Ajax Cape Town | 2:1 | ||
| 1st(1st leg): 14/03/2009 14:00 | 2nd (2nd leg): 05/04/2009 14:00 | Winner: Monomotapa United | ||||
| 1st(1st leg) | CD 1º de Agosto | - | Canon Yaoundé | 0:1 | ||
| 2nd (2nd leg) | Canon Yaoundé | - | CD 1º de Agosto | 4:5 pso | ||
| 1st(1st leg): 14/03/2009 15:00 | 2nd (2nd leg): 06/04/2009 15:00 | Winner: CD 1º de Agosto | ||||
| 1st(1st leg) | ASEC Mimosas | - | EF Ouagadougou | 2:0 | ||
| 2nd (2nd leg) | EF Ouagadougou | - | ASEC Mimosas | 0:1 | ||
| 1st(1st leg): 14/03/2009 15:30 | 2nd (2nd leg): 05/04/2009 19:00 | Winner: ASEC Mimosas | ||||
| 1st(1st leg) | Étoile du Sahel | - | ASO Chlef | 2:1 | ||
| 2nd (2nd leg) | ASO Chlef | - | Étoile du Sahel | 0:0 | ||
| 1st(1st leg): 14/03/2009 16:00 | 2nd (2nd leg): 03/04/2009 19:00 | Winner: Étoile du Sahel | ||||
| 1st(1st leg) | Heartland FC | - | FAR de Rabat | 3:1 | ||
| 2nd (2nd leg) | FAR de Rabat | - | Heartland FC | 1:1 | ||
| 1st(1st leg): 15/03/2009 14:00 | 2nd (2nd leg): 04/04/2009 16:00 | Winner: Heartland FC | ||||
| 1st(1st leg) | Coton Sport Garoua | - | DC Motema Pembe | 2:1 | ||
| 2nd (2nd leg) | DC Motema Pembe | - | Coton Sport Garoua | 2:3 | ||
| 1st(1st leg): 15/03/2009 14:00 | 2nd (2nd leg): 04/04/2009 | Winner: Coton Sport Garoua | ||||
| 1st(1st leg) | TP Mazembe | - | Petro Atlético | 3:0 | ||
| 2nd (2nd leg) | Petro Atlético | - | TP Mazembe | 1:2 | ||
| 1st(1st leg): 15/03/2009 14:30 | 2nd (2nd leg): 04/04/2009 | Winner: TP Mazembe | ||||
| 1st(1st leg) | Club Africain | - | Djoliba AC | 1:2 | ||
| 2nd (2nd leg) | Djoliba AC | - | Club Africain | 0:1 | ||
| 1st(1st leg): 15/03/2009 14:30 | 2nd (2nd leg): 05/04/2009 17:30 | Winner: Djoliba AC | ||||
| 1st(1st leg) | Asante Kotoko | - | Ittihad Khémisset | 3:1 | ||
| 2nd (2nd leg) | Ittihad Khémisset | - | Asante Kotoko | 2:0 | ||
| 1st(1st leg): 15/03/2009 15:00 | 2nd (2nd leg): 05/04/2009 15:30 | Winner: Ittihad Khémisset | ||||
| 1st(1st leg) | JS Kabylie | - | Al Ahly Tripolis | 1:2 | ||
| 2nd (2nd leg) | Al Ahly Tripolis | - | JS Kabylie | 1:0 | ||
| 1st(1st leg): 15/03/2009 15:00 | 2nd (2nd leg): 04/04/2009 18:00 | Winner: Al Ahly Tripolis | ||||
| 1st(1st leg) | Africa Sports | - | ZESCO United | 0:0 | ||
| 2nd (2nd leg) | ZESCO United | - | Africa Sports | 1:0 | ||
| 1st(1st leg): 15/03/2009 15:30 | 2nd (2nd leg): 04/04/2009 | Winner: ZESCO United | ||||
| 1st(1st leg) | Al Ahly SC | - | Young Africans | 3:0 | ||
| 2nd (2nd leg) | Young Africans | - | Al Ahly SC | 0:1 | ||
| 1st(1st leg): 15/03/2009 17:00 | 2nd (2nd leg): 04/04/2009 13:00 | Winner: Al Ahly SC | ||||
| 1st(1st leg) | Al Hilal Omdurman | - | US Stade Tamponnaise | 3:1 | ||
| 2nd (2nd leg) | US Stade Tamponnaise | - | Al Hilal Omdurman | 2:1 | ||
| 1st(1st leg): 15/03/2009 17:00 | 2nd (2nd leg): 05/04/2009 14:00 | Winner: Al Hilal Omdurman | ||||
