Two quick goals early in the second half from strikers Flavio and Manucho settled the contest.
Flavio scored his third of the tournament in the 48th minute while Manucho followed six minutes later with an opportunistic effort.
Flavio scored with a trademark header at the end of a storming run and cross from left back Mabina.
Manucho's strong physical presence proved vital as he stripped Malawi captain Peter Mponda of the ball on the edge of the Malawi penalty area and cracked home a powerful shot to make it 2-0.
Angola, who conceded four late goals to draw 4-4 with Mali on Sunday, head the group by a point from Algeria and Malawi and look well placed to take first place and stay in the capital for next week's quarter-finals.
The hosts, with a hard running approach, set out quickly to overwhelm their Malawian opponents, who enjoyed a surprise 3-0 win over Algeria in their first group game on Monday.
But only Djalma and Manucho had chances in the first half, thwarted by a lack of accuracy and a save by Malawi goalkeeper Swadick Sanudi.
A cheeky back heel almost saw Malawi go into the lead in the 41st minute but Victor Nyirenda's audacious effort was saved.
Angola's success will be tempered by concern over injury to key players Gilberto and Flavio, who both had to leave the game.
There were no late jitters this time as Angola comfortably held on their lead.
Their next game is against Algeria in Luanda on Monday.
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