كتب : Hatem Maher
The visitors went to the lockers room one up, thanks to a goal from striker Chiukepo Msowoya.
Two second-half goals from Moses Chavula and Atusaye Nyondo sealed the victory for Malawi.
Malawi have now nine points, just like Egypt and DR Congo, who face each other on Sunday.
Djibouti are rooted to the bottom after failing to bag a single point from five matches.
Six-time African champions Egypt would all but secure passage to the next round if they beat DR Congo in Kinshasa.
A draw would be favorable while a defeat might dent Egypt's hopes of booking a place in the World Cup finals for the first time since 1990.