Both goals came from Pretoria-based South African Premiership stars with veteran striker Dario Monteiro scoring on 30 minutes and midfielder Elias 'Domingues' Pelembe adding a second in the final minute.
Monteiro, of Mamelodi Sundowns, volleyed a cross past Malawi goalkeeper Swadic Sanudi and after the Mozambican Mambas missed several good scoring chances, Supersport United's Pelembe darted down the wing and cut inside to chip the ball into the net.
The decisive second goal came soon after substitute Manuel Fernandes was guilty of the miss of the match, heading meekly at Sanudi when unmarked a few yards from goal.
A lack of floodlights forced the organisers into an afternoon kick-off during a working day in the Mozambican capital and this restricted the attendance to about 2,000 spectators.
Mozambique host Nigeria on 29 March in the opening series of matches in the final African Zone qualifying phase for the 2010 FIFA World Cup in South Africa and Malawi play at Côte d'Ivoire the same day.