Senegal finished third in Group A with four points from three matches: one win, one draw and one defeat. Their campaign ended with a goalless draw against hosts Morocco in Rabat on Monday.
The result left the Lionesses behind Morocco and Algeria, who both advanced to the quarter-finals, while Kenya finished bottom of the group.
Cissé’s departure comes in the immediate aftermath of the group-stage elimination as the Senegal Football Federation begins assessing the team’s performance at the continental finals.