A penalty from Hosny Abd Rabou and a goal from Amir Zaki put holders Egypt through to the semi-final of the Africa Cup of Nations to meet Ivory Coast.
Abd Rabou converted his third spot-kick in Ghana on 20 minutes after Angola's Andre Macanga had handled in the area.
Manucho hit back shortly after with a 25-yard thunderbolt to equalise in a scintillating game in Kumasi.
But another defensive error from Kali allowed Zaki to bounce a cross off his chest and into the goal on 38 minutes.
Egypt progress to the next stage where they meet hotly-tipped Ivory Coast in Thursday's semi-final at the Baba Yara Stadium in Kumasi.