The Black Satellites scored a headed goal in each half in a lively game which saw plenty of opportunities for both sides.
Awako Gladson put Ghana ahead after 13 minutes with a fine header, before Osei Ransford found himself unmarked to nod home a deep ball on 77 minutes.
In Wednesday's second group game, hosts Rwanda came from a goal down to draw 1-1 with Cameroon.
Brice Owona drove home Cameroon's opener after a goal-mouth scramble on 35 minutes.
However, Yusuf Ndayishimiye equalised for Rwanda just 10 minutes later with a powerful header on the stroke of half-time.
Ghana and Rwanda are now both on four points, and the two may only need a draw as they meet in their remaining group game on Saturday.
Cameroon will need a win to stand any chance of progressing, as they meet Mali, who are out.
The top two teams in each group qualify for both the semi-finals and the Under-20 World Cup in Egypt.
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