Guinea played long balls that troubled the hosts. However, against the run of play, Chiukepo Msowoya scored for the hosts through a header on the half-hour mark after connecting a free-kick.
The lead did not last long as Lamine Yattara glanced in the equalized for Guinea seconds before the first half whistle.
Hopes of a Malawi come back were ended when Malawi youthful goalkeeper, Brighton Munthali, dropped a corner kick on the feet of Idrissa Sylla, who toe-poked into the net.
The Flames drop to the bottom of the group with two points from four games, whereas Guinea is at par with Swaziland with five points apiece, three points behind leaders, Zimbabwe.