The team that scored more goals on aggregate over the two legs advanced to the next round.
If the aggregate score was level, the away goals rule was applied, i.e. the team that scored more goals away from home over the two legs advanced.
If away goals were also equal, then extra time was not played and the winners were decided by a penalty shoot-out (Regulations III.
The mechanism of the draws for each round was as follows: The knockout stage involved the 8 teams which qualified as winners and runners-up of each of the four groups in the group stage.
The bracket of the knockout stage was determined as follows: The bracket was decided after the draw for the knockout stage, which was held on 12 March 2024, 15:00 CAT (UTC+2) at the CAF headquarters in Cairo, Egypt.