In form Malawi striker Chiukepo Msowoya and compatriot Dalitso Sailesi both scored in the first half as The Flames beat Sudan 2-1 in a Group C match.
Sudan could have levelled the scores in the dying minutes but wasted the penalties.
In another match in the same group played earlier,South Sudan registered their first cecafa win flying past minnows Djibouti by 2-0.
Bruno Martinez and Dominic Abuyo.
South Sudan tops the group with Malawi second with same points but shy on goal difference.
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