The 2016 CAF Champions League knockout stage was played from 16 September to 23 October 2016. A total of four teams competed in the knockout stage to decide the champions of the 2016 CAF Champions League.
The winners and runners-up of each of the two groups in the group stage qualified for the knockout stage. <section begin=Qualified teams /> <section end=Qualified teams />
<section begin=Format /> 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).<section end=Format />
The schedule of each round was as follows.
The bracket of the knockout stage was determined as follows:
<section begin=Bracket /> <section end=Bracket />
<section begin=Semi-finals /> 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.
<section end=Semi-finals />
Zamalek won 6âÂÂ5 on aggregate.
Mamelodi Sundowns won 3âÂÂ2 on aggregate.
<section begin=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.<noinclude>
</noinclude>
Mamelodi Sundowns won 3âÂÂ1 on aggregate.<section end=Final />