The Cranes had lost their opening game to Zambia and needed to bag maximum points on day two to revive their hopes
Uganda Cranes were dumped out of Chan 2018 after losing by a solitary goal to Namibia on Thursday night.
The Cranes had lost their opening game 1-3 to Zambia and needed to bag maximum points on day two to increase their chances of progressing in the competition.
The Namibians left it late once again as they handed the Cranes another painful defeat with Panduleni Nekundi scoring the crucial goal in injury time.
In the earlier game, Augustine Mulenga was the hero for Zambia as he scored a goal in each half to secure a 2-0 win over Ivory Coast.
The results mean that Namibia and Zambia go head-to-head on Monday to decide who tops the Group while Uganda and Ivory Coast are playing for pride.
Uganda dominated against Namibia, who dealt well with the pressure and always looked like they could create something on the counter-attack. Ugandan star Derrick Nsibambi was a threat for Namibia from onset and should have scored the opener in the 12th minute.
Nsibambi, who scored the lone goal against Zambia in their opening match, had the best chances in the second-half the first was well-saved by Loydt Kazapua while 12 minutes later he saw a shot from a tight angle go past the far post.
Kazapua was called into action again in the 68th minute with a good save from a fierce shot from outside the area from Allan Kyambadde. Ten minutes later, Uganda were reduced to ten men when Tim Awanyi was shown a second yellow card for a foul on Nekundi.
Nekundi then scored the winner in time added on when Uganda failed to clear a ball and he received it from Itamunua Keimuine to fire home the winner.
Namibia are competing for the first time after shocking Zimbabwe in a qualifier, and their preparations were hampered by the cancellation of their 2016/17 domestic league.
On Monday, Namibia play Zambia to decide, who finishes top of the group while Uganda and Ivory Coast will play for pride. Morocco and Sudan became the first teams to reach the quarters of the tournament for African players based in their own domestic leagues on Wednesday.
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