| 1. Round | 06/08/2003 | Cienciano | - | Alianza Lima | 1:0 | ||||
| 1. Round | 25/08/2003 | Alianza Lima | - | Cienciano | 0:1 | ||||
| Round of 16 | 24/09/2003 | Cienciano | - | Universidad Católica | 4:0 |  |
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| Round of 16 | 01/10/2003 | Universidad Católica | - | Cienciano | 3:1 | ||||
| Quarter-finals | 15/10/2003 | Santos FC | - | Cienciano | 1:1 | |
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| Quarter-finals | 28/10/2003 | Cienciano | - | Santos FC | 2:1 | |
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| Semi-finals | 12/11/2003 | Atlético Nacional | - | Cienciano | 1:2 | |
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| Semi-finals | 03/12/2003 | Cienciano | - | Atlético Nacional | 1:0 | ||||
| Final | 09/12/2003 | River Plate | - | Cienciano | 3:3 | ||||
| Final | 18/12/2003 | Cienciano | - | River Plate | 1:0 |  |
Paraguay