The final stages of the 2012 Copa Bridgestone Sudamericana de Clubes consisted of four stages:

• Round of 16 (first legs: September 25–27, October 2–3; second legs: October 23–25)^[1]
• Quarterfinals (first legs: October 30–November 1; second legs: November 7–8, 15)^[2]
• Semifinals (first legs: November 22; second legs: November 28–29)
• Finals (first leg: December 5; second leg: December 12)

The defending champion, Universidad de Chile, and the fifteen winners of the second stage (three from Argentina, four from Brazil, eight from rest of South America) qualified for the final stages. The sixteen teams played a single-elimination tournament, and were seeded depending on which second stage tie they won (i.e., the winner of Match O1 would be assigned the 1 seed, etc.; Universidad de Chile were assigned the 10 seed). In each stage, teams played in two-legged ties on a home-away basis, with the higher-seeded team playing the second leg at home. Each team earned 3 points for a win, 1 point for a draw, and 0 points for a loss. The following criteria were used for breaking ties on points, except for the final:^[3]

1. Goal difference
2. Away goals
3. Penalty shootout (no extra time is played)

For the final, the first tiebreaker was goal difference. If the teams are tied on goal difference, the away goals rule would not be applied, and 30 minutes of extra time would be played. If still had tied after extra time, the title would be decided by penalty shootout.

If two teams from the same association reach the semifinals, they would be forced to play each other.

In each tie, the higher-seeded team played the second leg at home.

	Round of 16						Quarterfinals						Semifinals						Finals
	1	Millonarios	1	3
	16	Palmeiras	3	0
							1	Millonarios	0	3
							8	Grêmio	1	1
	8	Grêmio	1	2
	9	Barcelona	0	1
													1	Millonarios	0	1
													4	Tigre (a)	0	1
	4	Tigre	0	4
	13	Deportivo Quito	2	0
							4	Tigre	0	4
							5	Cerro Porteño	1	2
	5	Cerro Porteño	2	2
	12	Colón	1	1
																			4	Tigre	0	0
																			2	São Paulo	0	2
	2	São Paulo (a)	1	0
	15	LDU Loja	1	0
							2	São Paulo	2	5
							10	U. de Chile	0	0
	7	Emelec	2	0
	10	U. de Chile	2	1
													2	São Paulo (a)	1	0
													11	U. Católica	1	0
	3	Liverpool	1	1
	14	Independiente	2	2
							14	Independiente	2	1
							11	U. Católica	2	2
	6	Atlético Goianiense	0	3
	11	U. Católica (a)	2	1

The Finals were played over two legs, with the higher-seeded team playing the second leg at home. If the teams were tied on points and goal difference at the end of regulation in the second leg, the away goals rule would not be applied and 30 minutes of extra time would be played. If still tied after extra time, the title would be decided by penalty shootout.^[3]

More information Tigre, 0–0 ...

Tigre	0–0	São Paulo
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More information São Paulo, 2–0 ...

São Paulo	2–0	Tigre
Lucas 22' Osvaldo 28'	Report

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The second leg was abandoned after 45 minutes by the referee, as the Tigre players refused to come back to play the rest of the match after incidents at halftime. Therefore, São Paulo were declared as the champion.^[4]

São Paulo won on points 4–1.