Draw
The draw for the second stage was held on 23 October 2020, 12:00 PYT (UTC−3). [4] For the second stage, the teams were allocated to two pots according to their previous results in this season: [5]
- Pot 1: 10 teams transferred from the Copa Libertadores and six best winners of the first stage from the Copa Sudamericana
- Pot 2: 16 remaining winners of the first stage from the Copa Sudamericana
The 32 teams were drawn into 16 ties (O1–O16) between a team from Pot 1 and a team from Pot 2, with the teams from Pot 1 hosting the second leg. Teams from the same association could be drawn into the same tie. The following are the 10 teams transferred from the Copa Libertadores (two best teams eliminated in the third stage of qualifying and eight third-placed teams in the group stage).
| Match | Best teams eliminated in third stage | Second stage draw |
|---|---|---|
| G3 |  Atlético Tucumán | Pot 1 |
| G4 |  Deportes Tolima | |
| Group | Third-placed teams in group stage | Second stage draw |
| A | Junior | Pot 1 |
| B |  Bolívar | |
| C |  Peñarol | |
| D |  São Paulo | |
| E |  Universidad Católica | |
| F |  Estudiantes de Mérida | |
| G | Defensa y Justicia | |
| H | Caracas |
The following are the 22 winners of the first stage from the Copa Sudamericana. Matches in the first stage were considered for the ranking of teams for the second stage draw.
| Pos | Match | First stage winners | Pld | W | D | L | GF | GA | GD | Pts | Second stage draw |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | E22 | Liverpool | 2 | 2 | 0 | 0 | 7 | 0 | +7 | 6 | Pot 1 |
| 2 | E8 | Bahia | 2 | 2 | 0 | 0 | 6 | 1 | +5 | 6 | |
| 3 | E3 |  Emelec | 2 | 2 | 0 | 0 | 5 | 0 | +5 | 6 | |
| 4 | E16 | Deportivo Cali | 2 | 2 | 0 | 0 | 5 | 2 | +3 | 6 | |
| 5 | E6 | River Plate | 2 | 2 | 0 | 0 | 3 | 1 | +2 | 6 | |
| 6 | E19 | Huachipato | 2 | 2 | 0 | 0 | 2 | 0 | +2 | 6 [a] | |
| 7 | E11 |  Sol de América | 2 | 2 | 0 | 0 | 2 | 0 | +2 | 6 [a] | Pot 2 |
| 8 | E10 | Atlético Nacional | 2 | 1 | 1 | 0 | 4 | 1 | +3 | 4 | |
| 9 | E12 | Sportivo Luqueño | 2 | 1 | 1 | 0 | 5 | 4 | +1 | 4 | |
| 10 | E9 | Fénix | 2 | 1 | 1 | 0 | 3 | 2 | +1 | 4 | |
| 11 | E2 | Vasco da Gama | 2 | 1 | 1 | 0 | 1 | 0 | +1 | 4 | |
| 12 | E1 | Coquimbo Unido | 2 | 1 | 0 | 1 | 3 | 1 | +2 | 3 [b] | |
| 13 | E4 | Plaza Colonia | 2 | 1 | 0 | 1 | 3 | 1 | +2 | 3 [b] | |
| 14 | E15 | Lanús | 2 | 1 | 0 | 1 | 3 | 2 | +1 | 3 [c] | |
| 15 | E20 | Audax Italiano | 2 | 1 | 0 | 1 | 3 | 2 | +1 | 3 [c] | |
| 16 | E7 | Unión | 2 | 1 | 0 | 1 | 3 | 2 | +1 | 3 [c] | |
| 17 | E14 | Millonarios | 2 | 1 | 0 | 1 | 2 | 1 | +1 | 3 | |
| 18 | E5 |  Melgar | 2 | 1 | 0 | 1 | 2 | 2 | 0 | 3 [d] | |
| 19 | E21 | Independiente | 2 | 1 | 0 | 1 | 2 | 2 | 0 | 3 [d] | |
| 20 | E13 | Vélez Sarsfield | 2 | 1 | 0 | 1 | 2 | 2 | 0 | 3 [d] | |
| 21 | E17 | Sport Huancayo | 2 | 0 | 2 | 0 | 1 | 1 | 0 | 2 [e] | |
| 22 | E18 | Unión La Calera | 2 | 0 | 2 | 0 | 1 | 1 | 0 | 2 [e] |
Rules for classification: 1) Points; 2) Goal difference; 3) Goals scored; 4) Away goals scored; 5) CONMEBOL ranking.
Notes:
- 1 2 CONMEBOL ranking: Huachipato 98, Sol de América 109.
- 1 2 CONMEBOL ranking: Coquimbo Unido 191, Plaza Colonia unranked.
- 1 2 3 CONMEBOL ranking: Lanús 26, Audax Italiano 137, Unión unranked.
- 1 2 3 Away goals scored: Melgar 2, Independiente 1, Vélez Sarsfield 1. CONMEBOL ranking: Independiente 20, Vélez Sarsfield 32.
- 1 2 CONMEBOL ranking: Sport Huancayo 198, Unión La Calera unranked.
