Kenya finished top of Group A thanks to striker Ryan Ogam’s 75th-minute goal in Nairobi.
The home team already had one foot in the knock-out phase heading into the final round of group matches, knowing avoiding defeat would guarantee progress.
Morocco grabbed second place in the group and a last-eight berth courtesy of a 3-1 victory over the Democratic Republic of Congo in a winner-takes-all clash.
Berkane forward Oussama Lamlioui scored in the eighth minute to put Morocco, who were level on six points with their opponents before kick-off, into the lead.
