The 2016 CAF Confederation Cup knockout stage was played from 17 September to 6 November 2016.[1] A total of four teams competed in the knockout stage to decide the champions of the 2016 CAF Confederation Cup.[2]
The winners and runners-up of each of the two groups in the group stage qualified for the knockout stage.
| Group | width=200 | Winners | width=200 | Runners-up |
|---|---|---|---|---|
| A |  TP Mazembe | MO Béjaïa | ||
| B |  FUS Rabat |  Étoile du Sahel |
In the knockout stage, the four teams played a single-elimination tournament. Each tie was played on a home-and-away two-legged basis. If the aggregate score was tied after the second leg, the away goals rule would be applied, and if still tied, extra time would not be played, and the penalty shoot-out would be used to determine the winner (Regulations III. 26 & 27).[2]
The schedule of each round was as follows.[1]
| Round | First leg | Second leg | |
|---|---|---|---|
| Semi-finals | 16–18 September 2016 | 23–25 September 2016 | |
| Final | 28–30 October 2016 | 4–6 November 2016 |
The bracket of the knockout stage was determined as follows:[2]
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.
|}
1–1 on aggregate. TP Mazembe won on away goals.----1–1 on aggregate. MO Béjaïa won on away goals.
See main article: article and 2016 CAF Confederation Cup Final. In the final, the two semi-final winners played each other, with the order of legs decided by an additional draw held after the group stage draw.[3]
|}TP Mazembe won 5–2 on aggregate.