Cisse was admitted on Friday following his team's 3-1 victory over Cameroon at the tournament in the Ivory Coast but is now back with the squad at their hotel in the Ivorian capital.
"He was treated by the medical staff and care services of Yamoussoukro hospital for a benign infection," said the Senegalese Football Federation on Saturday.
Cisse was admitted hours after Senegal won their second game at the tournament, a result that secured them a place in the next round.
Cisse has been coach of his country since 2015 and led them to victory at the last Cup of Nations two years ago. He also coached them at the last two World Cup finals.
Meanwhile, striker Sima is out of the tournament after suffering an injury in training on Wednesday.
"Abdallah Sima left today after examinations following an injury contracted during training on Wednesday. He has an injury to the long adductor of the left thigh," a statement said.
"Presuming a long period of unavailability of the player, the medical staff of the Senegal team and his club, Glasgow Rangers, have decided to return him to the club for optimal management of his injury."
Sima had been a late call-up by the defending champions.
