كتب : Omar AbdelAziz
Russell Mwafulirwa scored twice to steer the home side to victory after Lomana Lua-Lua's early opener for Congo.
Malawi claim top spot temporarily as they levelled on 12 points with Egypt, but the former have a better goal difference so far.
However, the African champions are expected to ease past minnows Djibouti at Cairo Stadium on Sunday.
Malawi are ensured a place in the final phase of the qualifiers as one of eight second-best finsihers in the second round.