The result coupled with Nigeria’s 1-0 win over Kenya, also on Wednesday, sees Malawi in second place in Group F on six points while the draw for Namibia sees them on four points in third spot.
The Flames, though, will see it as a missed opportunity, especially as Nigeria scored late on against Kenya to take command of the pool.
It means Malawi will likely have to win their last two qualifiers, one of which is in Abuja.
Malawi coach Eddington Ngonamo was able to field a strong line-up that included most of his South African-based stars, but the match was a rather dull affair with few chances on goal for either side.
Instead, it was a game characterised by wasteful passing and poor decision making in the final third of the field.
If either team is to improve on their standings in the group they will have to work on their finishing which was extremely poor on the day.