The Second Stage of the 2009 Copa Santander Libertadores was a group stage. It was played from February 10 to April 30.

Twenty-six teams qualified directly into this round, plus six that advanced from the First Stage. This brings the total number of teams in the Second Stage to 32. The teams were drawn into eight groups of four. The teams in each group will play each other in a double round-robin format, playing the other teams in the group once at home and once away. Teams will be awarded 3 points for a win, 1 point for a draw, and 0 points for a loss. The following criteria will be used for breaking ties on points:

1. Goal difference
2. Goals scored
3. Away goals
4. Draw

The top two teams from each group advance to the Round of 16.

Pos	Team	Pld	W	D	L	GF	GA	GD	Pts		RFE	PAL	CC	LDU
1	Sport Recife	6	4	1	1	10	7	+3	13		—	0–2	2–1	2–0
2	Palmeiras	6	3	1	2	9	7	+2	10		1–1	—	1–3	2–0
3	Colo-Colo	6	2	1	3	9	7	+2	7		1–2	0–1	—	3–0
4	LDU Quito	6	1	1	4	6	13	−7	4		2–3	3–2	1–1	—

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Pos	Team	Pld	W	D	L	GF	GA	GD	Pts		BOC	CUE	TÁC	GDL
1	Boca Juniors	6	5	0	1	11	3	+8	15		—	1–0	3–0	3–1
2	Deportivo Cuenca	6	3	1	2	9	4	+5	10		1–0	—	3–1	4–0
3	Deportivo Táchira	6	3	0	3	6	9	−3	9		0–1	1–0	—	2–1
4	Guaraní	6	0	1	5	5	15	−10	1		1–3	1–1	1–2	—

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Pos	Team	Pld	W	D	L	GF	GA	GD	Pts		NAC	USM	RIV	NPR
1	Nacional	6	4	2	0	12	3	+9	14		—	2–1	3–0	3–1
2	Universidad San Martín	6	2	2	2	7	9	−2	8		1–1	—	2–1	2–1
3	River Plate	6	2	1	3	7	9	−2	7		0–0	3–0	—	1–0
4	Nacional	6	1	1	4	7	12	−5	4		0–3	1–1	4–2	—

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Pos	Team	Pld	W	D	L	GF	GA	GD	Pts		SPO	DEF	DIM	AMC
1	São Paulo	6	4	1	1	10	6	+4	13		—	2–1	1–1	2–1
2	Defensor Sporting	6	2	2	2	5	5	0	8		0–1	—	4–3	1–0
3	Independiente Medellín	6	1	4	1	6	6	0	7		2–1	0–0	—	0–0
4	América de Cali	6	0	3	3	3	7	−4	3		1–3	0–0	1–1	—

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Pos	Team	Pld	W	D	L	GF	GA	GD	Pts		CRU	ELP	QUI	UNI
1	Cruzeiro	6	4	1	1	9	5	+4	13		—	3–0	2–0	2–0
2	Estudiantes	6	3	1	2	9	4	+5	10		4–0	—	4–0	1–0
3	Deportivo Quito	6	2	2	2	6	9	−3	8		1–1	1–0	—	3–1
4	Universitario de Sucre	6	0	2	4	2	8	−6	2		0–1	0–0	1–1	—

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Pos	Team	Pld	W	D	L	GF	GA	GD	Pts		CAR	GDL	EVE	LAN
1	Caracas	6	3	1	2	7	4	+3	10		—	2–0	1–0	3–1
2	Guadalajara	6	2	3	1	9	6	+3	9		1–0	—	6–2	0–0
3	Everton	6	2	2	2	7	10	−3	8		1–0	1–1	—	1–1
4	Lanús	6	0	4	2	5	8	−3	4		1–1	1–1	1–2	—

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Pos	Team	Pld	W	D	L	GF	GA	GD	Pts		GRÊ	UCH	BOY	AUR
1	Grêmio	6	5	1	0	11	1	+10	16		—	0–0	3–0	3–0
2	Universidad de Chile	6	3	1	2	8	6	+2	10		0–2	—	3–0	3–0
3	Boyacá Chicó	6	3	0	3	8	8	0	9		0–1	3–0	—	2–1
4	Aurora	6	0	0	6	3	15	−12	0		1–2	1–2	0–3	—

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Pos	Team	Pld	W	D	L	GF	GA	GD	Pts		LIB	SLU	UNI	SLO
1	Libertad	6	4	0	2	7	5	+2	12		—	0–2	2–1	2–0
2	San Luis	6	2	2	2	7	7	0	8		0–1	—	2–2	2–0
3	Universitario	6	2	2	2	6	7	−1	8		2–1	0–0	—	1–0
4	San Lorenzo	6	2	0	4	6	7	−1	6		0–1	4–1	2–0	—

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• CONMEBOL's official website (in Spanish)