Angola's first win of the tournament was preceded by a close-fought 1-0 win for Algeria over Mali, setting up the group for a dramatic finish on Monday.
Striker Flavio scored a third goal of the tournament to put Angola ahead just after halftime and Manucho added a second soon after as the hosts banished the image of their dramatic capitulation on Sunday when they conceded four late goals to draw 4-4 with Mali.
"We have the spirit and the right attitude and we always knew we were going to win," said coach Manuel Jose after the victory, which put Angola top with four points.
Malawi are second, just ahead of Algeria on goal difference, on three points with Mali on a single point, but still in with a chance of progressing to the last eight.
Angola showed few jitters on Thursday in stark contrast to Sunday's opening match.
A win over Algeria in their last game would ensure Angola stay in the capital for the quarter-finals.
"That would be the logical ambition for us because this is our home, we are settled and we have such great support," Jose added.
Malawi can still hope for a surprise quarter-final place, but will have to avoid defeat against Mali to stand any chance. The two teams play in Cabinda on Monday.
"We believe that we can control that game and go on and win," midfielder Joseph Kamwendo told Reuters.
Algeria would have been the first team eliminated from the tournament had they lost to Mali on Thursday, but instead won by a single goal, scored just before halftime by defender Rafik Halliche.
The win by the Algerians was the first from a World Cup-bound team at the Nations Cup. Two others, Ghana and the Ivory Coast, meet in Group B in Cabinda on Friday.
