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The Flying Eagles suffered a disappointing 2-1 defeat at the hands of the minnows in what was an entertaining game at the Accra Sports Stadium.
Ladan Bosso’s side didn’t look troubled in the opening exchanges but fell behind against the run of play in the 13th minute following a smart finish from Kiza Usama.
Nigeria shocked by Uganda in African Games opener
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Nigeria upped the ante after falling behind but their best efforts were constantly repelled by the resilient defence of the Ugandans.
The Flying Eagles, however, got their breakthrough with seven minutes left to the end of the first half, thanks to Sadiq Muhammad’s strike.
Despite both teams creating some decent chances in the second half, it was Uganda who had the last laugh after Ivan Irinibabazi scored late in the game to hand them a 2-1 victory.
Meanwhile, the other Group B game also saw Senegal record a narrow 1-0 victory over South Sudan to move to the top of the group.
The men’s football competition of the African Games will continue on Friday, with hosts Ghana taking on Congo while Benin will also face the Gambia in the other Group A game.