The knockout phase involves the sixteen teams who finished in the top two in each of their groups in the group stage. Each tie in the knockout phase, apart from the final, is played over two legs, with each team playing one leg at home. The team that has the higher aggregate score over the two legs progresses to the next round. In the event that aggregate scores finish level, the away goals rule is applied, i.e. the team that scored more goals away from home over the two legs progresses. If away goals are also equal, then thirty minutes of extra time are played, divided into two fifteen-minutes halves. The away goals rule is again applied after extra time, i.e. if there are goals scored during extra time and the aggregate score is still level, the visiting team qualifies by virtue of more away goals scored. If no goals are scored during extra time, the tie is decided by penalty shootout. In the final, the tie is played as a single match. If scores are level at the end of normal time in the final, extra time is played, followed by penalties if scores remain tied. In the draw for the round of 16, the eight group winners are seeded, and the eight group runners-up are unseeded. A seeded team is drawn against an unseeded team, with the seeded team hosting the second leg. Teams from the same group or the same association cannot be drawn against each other. In the draws for the quarter-finals onwards, there are no seedings, and teams from the same group or the same association may be drawn with each other.
The first legs were played on 14, 15, 21 and 22 February, and the second legs were played on 6, 7, 13 and 14 March 2012.
First leg
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Second leg
Milan won 4–3 on aggregate. ---- Benfica won 4–3 on aggregate. ---- 1–1 on aggregate. APOEL won 4–3 on penalties. ---- Barcelona won 10–2 on aggregate. ---- 2–2 on aggregate. Marseille won on away goals. ---- Bayern Munich won 7–1 on aggregate. ---- Chelsea won 5–4 on aggregate. ---- Real Madrid won 5–2 on aggregate.
Quarter-finals
The first legs were played on 27 and 28 March, and the second legs were played on 3 and 4 April 2012.
First leg
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Second leg
Bayern Munich won 4–0 on aggregate. ---- Barcelona won 3–1 on aggregate. ---- Real Madrid won 8–2 on aggregate. ---- Chelsea won 3–1 on aggregate.
Semi-finals
The first legs were played on 17 and 18 April, and the second legs were played on 24 and 25 April 2012.
First leg
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Second leg
Chelsea won 3–2 on aggregate. ---- 3–3 on aggregate. Bayern Munich won 3–1 on penalties.