| Group 1 | 12/04/2006 | Caracas FC | - | Deportivo Guadalajara | 0:0 | ||||
| Group 1 | 21/04/2006 | Deportivo Guadalajara | - | Cienciano | 0:0 | ||||
| Round of 16 | 03/05/2006 | Santa Fe | - | Deportivo Guadalajara | 3:1 | ||||
| Quarter-finals | 10/05/2006 | Deportivo Guadalajara | - | Vélez Sarsfield | 0:0 | ||||
| Quarter-finals | 21/07/2006 | Vélez Sarsfield | - | Deportivo Guadalajara | 1:2 | ||||
| Semi-finals | 27/07/2006 | Deportivo Guadalajara | - | São Paulo FC | 0:1 | ||||
| Semi-finals | 03/08/2006 | São Paulo FC | - | Deportivo Guadalajara | 3:0 |  |
Mexico