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. The mechanism of the draws for each round is as follows:
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 12, 13, 19 and 20 February, and the second legs were played on 5, 6, 12 and 13 March 2013.
First leg
---- ---- A minute's silence was held before the match to commemorate the victims of the crash of South Airlines Flight 8971, which had been filled mostly with football fans heading for the match. ---- ---- ---- ---- ----
Second leg
---- Real Madrid won 3–2 on aggregate. ---- Borussia Dortmund won 5–2 on aggregate. ---- Paris Saint-Germain won 3–2 on aggregate. ---- Juventus won 5–0 on aggregate. ---- Galatasaray won 4–3 on aggregate. ---- Barcelona won 4–2 on aggregate. ---- Málaga won 2–1 on aggregate. ---- 3–3 on aggregate. Bayern Munich won on away goals.
Quarter-finals
The first legs were played on 2 and 3 April, and the second legs were played on 9 and 10 April 2013.
First leg
---- ---- ----
Second leg
---- Borussia Dortmund won 3–2 on aggregate. ---- Real Madrid won 5–3 on aggregate. ---- 3–3 on aggregate. Barcelona won on away goals. ---- Bayern Munich won 4–0 on aggregate.
Semi-finals
The first legs were played on 23 and 24 April, and the second legs were played on 30 April and 1 May 2013.
First leg
---- ----
Second leg
---- Borussia Dortmund won 4–3 on aggregate. ---- Bayern Munich won 7–0 on aggregate.
Final
The final was played on 25 May 2013 at Wembley Stadium in London, England.
Paris Saint-Germain
Porto
Schalke 04
Arsenal
Málaga
Milan
Shakhtar Donetsk
Celtic
Galatasaray