The Scorchers, who stunned defending champions Nigeria 3-2 in their opening match, made it two wins from two despite playing much of the second half with 10 players after R. Alufandika was sent off in the 52nd minute.
R. Kadzere opened the scoring in the 35th minute, converting a pass from Temwa Chawinga. F. Chinzimu doubled the lead deep in first-half stoppage time to give Malawi a 2-0 advantage at the break.
After the red card, Temwa Chawinga restored the three-goal cushion in the 68th minute with a well-taken finish, assisted by Kadzere. Egypt pulled one back three minutes later through I. Hassan, but Malawi held firm to secure all three points.
The result leaves Malawi top of Group C with six points from two matches and a strong chance of reaching the quarter-finals. Egypt remain bottom with zero points after suffering a second heavy defeat, having lost 6-0 to Zambia in their opener.
Malawi will face Zambia in their final group match on Wednesday, while Egypt take on Nigeria.