The knock-out stage of the 2013 CAF Confederation Cup was played from 6 October to 30 November 2013. A total of four teams competed in the knock-out stage.[1]
The winners and runners-up of each of the two groups in the group stage qualified for the knock-out stage.
| Group | width=190 | Winners | width=190 | Runners-up |
|---|---|---|---|---|
| A |  CS Sfaxien |  Stade Malien | ||
| B |  TP Mazembe | CA Bizertin |
Knock-out ties were played on a home-and-away two-legged basis. If the sides were level on aggregate after the second leg, the away goals rule was applied, and if still level, the tie proceeded directly to a penalty shoot-out (no extra time was played).[1]
The schedule of each round was as follows.[2]
| Round | First leg | Second leg | |
|---|---|---|---|
| Semi-finals | 4–6 October 2013 | 18–20 October 2013 | |
| Final | 22–24 November 2013 | 29 November–1 December 2013 |
In the semi-finals, the group A winners played the group B runners-up, and the group B winners played the group A runners-up, with the group winners hosting the second leg.[1]
|}
CS Sfaxien won 1–0 on aggregate and advanced to the final.----TP Mazembe won 3–1 on aggregate and advanced to the final.
See main article: 2013 CAF Confederation Cup Final.
In the final, the order of legs was decided by a draw.[3] The draw was held on 14 May 2013, 14:00 UTC+2, at the CAF Headquarters in Cairo, Egypt.
|}
CS Sfaxien won 3–2 on aggregate.