The 2012–13 UAFA Club Cup knock-out stage matches took place from 8 February to 14 May 2013. A total of 8 teams competed in the knock-out stage to decide the champions of the 2012–13 UAFA Club Cup.
All knock-out ties were decided over two legs, with aggregate goals used to determine the winner. If the sides were level on aggregate after the second leg, the away goals rule applied, and if still level, the tie proceeded to a penalty shootout after extra time is played.
The schedule of each round was as follows.[1]
| Round | First leg | Second leg | |
|---|---|---|---|
| Quarter-finals | 8–13 February 2013 | 26–27 February 2013 | |
| Semi-finals | 12 March 2013 | 2–3 April 2013 | |
| Final | 24 April 2013 | 14 May 2013 |
The knock-out stage featured eight teams: four from Africa zone and four from Asia zone took place in quarterfinals.
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Raja Casablanca won 3–1 on aggregate.----
USM Alger won 9–3 on aggregate.----
Ismaily SC won 4–1 on penalties.----
Al-Arabi won 4–3 on aggregate.
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USM Alger won 4–3 on penalties.----
On aggregate 3–3. Al-Arabi won on away goals rule.
See main article: 2013 UAFA Club Cup Final. |}
USM Alger won 3–2 on aggregate.
