The aerial prowess of the Shabab striker, who scored twice in Angola's 4-4 draw against Mali with superb headers, once again gave Angola the lead in the Group A encounter.
He was carried off on a stretcher three minutes past the hour mark after picking up an injury, making way for Mantorras.
Real Valladolid frontman and Flavio's partner Manucho sealed Angola's win nine minutes after the restart.
Angola lead the group with four points, one ahead of Malawi and Algeria, who beat Mali 1-0 earlier in the day.
Mali, who couldn't build on their remarkable comeback against Angola, lie at the bottom on one point.
A draw for Angola in their last group-stage game against Algeria on Monday will be enough to send them to the knockout phase.
Too Good
Flavio, who left Egyptian champions Ahli in the close season, proved too good for Malawi's defenders, unsettling them with his smart moves.
Angola's lively winger Mabina was also a constant menace to defenders with his penetration abilities and inch-perfect crosses.
Manucho spurned a glorious opportunity to fire Manuel Jose's ahead in the 34th minute when he broke clear on goal before Malawi keeper Swadick Sanudi blocked his shot.
Ahli winger Gilberto, who produced a fine display in the draw with Mali, left the pitch before the break after seemingly sustaining an injury.
Angola's pressure paid dividends on 48 minutes when Mabina, who was switched to the left flank in the second half after Gilberto was substituted, whipped in a pinpoint cross for Flavio to head home.
Manucho wrapped up the victory in the 54th minute when he robbed Peter Mponda on the edge of the area before smashing a left-footed shot past Sanudi.