The Black Stars, who have just one point from two matches, sit third in Group F. Angola and Sudan are joint leaders after winning their respective opening games, and are set to face off later on Sunday.
Alidu Seidu put Ghana ahead just before halftime, scoring in the 44th minute. However, Oumar Sako netted a crucial equalizer for Niger in the 81st minute, securing a point for the hosts.
Ghana had previously suffered a 1-0 defeat at home to Angola in their opening match on Thursday.
In Group K, Uganda claimed a 2-0 win over Congo with goals from Abdu Kayondo (21) and Jude Ssemugabi (86), moving them to the top of the group with four points. Congo sit second with three points.
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