Keita snubbed Pepe and then threw a water bottle at him, which appeared to hit the Portugal defender on the shoulder.
Goalkeeper Vincent Enyeama, defender Efe Ambrose, midfielders John Obi Mikel and Victor Moses and striker Emmanuel Emenike were selected after the Super Eagles defeated Burkina Faso 1-0 in the final.
Barcelona says midfielder Seydou Keita has told the Spanish club he wants to leave the team.
Barcelona centre-back Gerard Pique has been banned for one match following his dismissal against Sporting Gijon at the weekend, the Spanish Football Federation (RFEF) announced on Wednesday.
Seydou Keita and Xavi Hernandez came to the rescue to give 10-man Barcelona a crucial 3-1 victory over Sporting Gijon on Saturday which cut the gap on leaders Real Madrid to seven points.
Barcelona midfielder Seydou Keita returned on Saturday to the Mali squad for first time since his self-imposed exile from international football after the 2010 Africa Cup of Nations.
Mali international midfielder Seydou Keita scored only his second goal of the season as champions Barcelona moved ten points clear of Real Madrid in the Spanish first division with a hard-fought 1-0 home win over Real Zaragoza on Saturday.