| Thursday 12th March 2009 | |||
| 1st Leg | |||
| CSKA Moscow | 1-0 | Shakhtar Donetsk | |
| Dinamo Kiev | 1-0 | Metalist Kharkiv | |
| Manchester City | 2-0 | AaB Aalborg | |
| Marseille | 2-1 | Ajax | |
| Paris Saint-Germain | 0-0 | Sporting Braga | |
| SV Hamburg | 1-1 | Galatasaray | |
| Udinese | 2-0 | Zenit St Petersburg | |
| Werder Bremen | 1-0 | Saint-Etienne | |
| Wednesday 18th March 2009 | |||
| 2nd Leg | |||
| Ajax | 2-2 | Marseille | aet (3-4) |
| Saint-Etienne | 2-2 | Werder Bremen | (2-3) |
| Thursday 19th March 2009 | |||
| 2nd Leg | |||
| AaB Aalborg | 2-0 | Manchester City | aet (2-2) |
| (Manchester City won on penalties) | |||
| Galatasaray | 2-3 | SV Hamburg | (3-4) |
| Metalist Kharkiv | 3-2 | Dinamo Kiev | (3-3) |
| (Dinamo Kiev won on away goals) | |||
| Shakhtar Donetsk | 2-0 | CSKA Moscow | (2-1) |
| Sporting Braga | 0-1 | Paris Saint-Germain | (0-1) |
| Zenit St Petersburg | 1-0 | Udinese | (1-2) |
