Striker Gabadinho Mhango put Malawi ahead with a 10th-minute penalty before adding the second in the 34th minute, which also came from the spot.
The visitors narrowed the gap seven minutes after the hour-mark when Abubeker Nasir converted another penalty but Malawi held on for all three points to move top of Group D.
Egypt will host Guinea later in the day in Cairo.
In Group J, Tunisia were held to a goalless draw by Botswana to remain in the…
