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 driving seat of the group with four points, one ahead of second-placed Libya, who visit Equatorial Guinea on Monday.
Tunisia hammered Equatorial Guinea 4-0 at home in their group opener on Thursday.
Earlier in the day, Ghana played out a 1-1 away draw with Central Africa in Group E.
Mohammed Kudus gave the Black Stars a 17th-minute lead but Central Africa's Karl Namnganda levelled the score four minutes before the break.
Ghana top the group with four points, on level with Angola who drew 1-1 with Madagascar on Sunday.
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