"Adama Niane was excluded from the Eagles group for non-respect," said the team's media officer Ibrahim Zie Coulibaly.
Reports said the 26-year-old Belgian-based player had slapped a team mate in an altercation over queuing.
The decision came on the eve of Friday's Group E match against Tunisia in Suez.
Burundi sent home 32-year-old midfielder Selemani Ndikumana for ill-discipline before their first game without offering any further details. On Wednesday Egypt sent Amr Warda packing for what the Egypt Football Association described as "disciplinary reasons".
Warda, who plays for Greek club Atromitos on loan from PAOK, has been widely accused of trolling women on social media and has been the subject of a previous complaint, filed with Egypt's Attorney General, of harassing a fashion model on Instagram.
Warda has since posted a video on Facebook in which he apologised to his family, his team mates, to the EFA and to "anyone who is upset at me or anyone I have upset" as his team mates rallied around him.
Among them was Mohamed Salah who said: "Women must be treated with the utmost respect but I also believe that many who make mistakes can change for the better and shouldn't be sent straight to the guillotine, which is the easiest way out.
"We need to believe in second chances... we need to guide and educate. Shunning is not the answer."
(Reporting by Mark Gleeson; Editing by Christian Radnedge)
