| Qualifier | 28/09/1999 | CF América | - | Atlas Guadalajara | 2:0 | ||||
| Qualifier | 18/10/1999 | Deportivo Táchira | - | Atlas Guadalajara | 2:2 | ||||
| Qualifier | 26/10/1999 | Atlas Guadalajara | - | CF América | 6:3 |  |
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| Qualifier | 10/11/1999 | Atlas Guadalajara | - | Deportivo Táchira | 3:0 | ||||
| Qualifier | 17/11/1999 | Atlas Guadalajara | - | CD Italchacao | 2:2 | |
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| Group 4 | 22/02/2000 | Atlas Guadalajara | - | River Plate | 1:1 | ||||
| Group 4 | 28/02/2000 | Atlético Nacional | - | Atlas Guadalajara | 2:3 | |
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| Group 4 | 07/03/2000 | Atlas Guadalajara | - | Universidad de Chile | 0:0 | ||||
| Group 4 | 14/03/2000 | River Plate | - | Atlas Guadalajara | 3:2 |  |
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| Group 4 | 21/03/2000 | Atlas Guadalajara | - | Atlético Nacional | 5:1 | ||||
| Group 4 | 19/04/2000 | Universidad de Chile | - | Atlas Guadalajara | 3:2 | ||||
| Round of 16 | 02/05/2000 | Atlas Guadalajara | - | Atlético Junior | 2:0 | ||||
| Round of 16 | 09/05/2000 | Atlético Junior | - | Atlas Guadalajara | 1:3 | ||||
| Quarter-finals | 17/05/2000 | Atlas Guadalajara | - | Palmeiras | 0:2 | ||||
| Quarter-finals | 24/05/2000 | Palmeiras | - | Atlas Guadalajara | 3:2 | |
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Mexico