Uganda's expulsion follows a similar punishment for neighbours Kenya last month.
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The punishment was handed out because it was discovered Uganda fielded a player who had supplied two different dates of birth in the qualifying tie with Rwanda, which they won 3-2 on aggregate.
Goalkeeper James Ahebwa had been registered to play for Ugandan club SC Villa in the African Champions League two years ago, using a birth date of 1997.
Yet for the under-20 qualifiers, he produced a passport that stated he was born in 1998.
Rwanda will instead now play Egypt in the second round of the preliminaries next weekend.
Last month, Kenya were thrown out for fielding five over-age players in their tie with Sudan.
Age cheating is notorious in African football but offending football associations are rarely caught or punished.
(Reporting by Mark Gleeson in Cape Town, editing by Ian Chadband)
