See main article: 2009 Copa Libertadores.
The First Stage of the 2009 Copa Santander Libertadores ran from January 27 to February 5.
Twelve teams qualified into this rounds and each will play a two-legged tie, one at home and one away. The winner of each tie will advance to the Second Stage. The teams will earn 3 points for a win, 1 point for a draw, and 0 for a loss. The team with the most points advances. The following criteria will be used for breaking ties on points:
Team #1 played the first leg at home.
| Teams | Scores | Tie-breakers | ||||||
|---|---|---|---|---|---|---|---|---|
| Team #1 | Team #2 | 1st leg | 2nd leg | |||||
| 1:4 |  Independiente Medellín | 0–4 | 0–0 | — | — | — | ||
Estudiantes  | 3:3 | 1–2 | 1–0 | 0:0 | 1:0 | — | ||
| Nacional | 4:1 |  El Nacional | 5–0 | 3–3 | — | — | — | |
| Deportivo Cuenca | 3:3 |  Deportivo Anzoátegui | 0–2 | 3–0 | +1:−1 | — | — | |
Real Potosí  | 0:6 |  Palmeiras | 1–5 | 0–2 | — | — | — | |
Pachuca  | 3:3 | Universidad de Chile | 0–1 | 2–1 | 0:0 | 0:1 | — | |
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Independiente Medellín advances on points 4–1.----Deportivo Cuenca advances on goal difference.----Estudiantes advances on away goals.----Palmeiras advances on points 6–0.----Universidad de Chile advances on away goals.----Nacional advances on points 4–1.