Koffi Dankowa and Moussa Maazou scored for Niger before Andile Jali reduced arrears in a 2-1 Niamey triumph that took them top of Group G, while three points against Egypt in Cairo during October will ensure them of first place.
Manucho headed home an early second-half cross for Angola, while veteran striker Flavio added a second as persistent pressure created cracks in the Ugandan defence.
Emmanuel Mayuka scored three minutes from full-time to secure a 2-1 win for Zambia on the Comoros Islands which took his country a point above Libya before an October match in Lusaka that will decide who wins Group C.
Morocco hit the crossbar and a post and had a goal disallowed during a 0-0 draw in the Central African Republic with the result lifting both teams on to eight points in Group D - three clear of Tanzania and Algeria.
Unbeaten Sudan joined 2010 Africa Cup of Nations runners-up Ghana at the Group I summit with a 1-0 victory in Congo Brazzaville courtesy of a Bakry Abdelgadir goal 13 minutes from full-time.
Zimbabwe kept alive slim hopes of winning Group A with a 3-0 home win over Liberia, while Faty Papy scored in the final minute to salvage a 1-1 draw for Burundi with visiting Benin.