Goals from Batiibwe Okello and Hakim Mutebi ensured the Morley Byekwaso-coached side beat the tournament hosts to the trophy in front of their fans.
Uganda needed to come from behind to edge neighbours Kenya 2-1 to win the CECAFA U18 championship at the Jomo Kenyatta Stadium, Kisumu, on Friday.
Goals from Batiibwe Okello and Hakim Mutebi ensured the Morley Byekwaso-coached side beat the tournament hosts to the trophy in front of their fans.
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Syphas Owuor had given Kenya the lead in the second half before Uganda fought back to victory.
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Following a cagey first half that was limited in goal-scoring opportunities, the second was the opposite as both sides returned to notch a possible winner.
Kenya then broke the deadlock in the 66th minute through a well-taken Syphas Owuor goal following a long ball from goalkeeper Ibrahim Wanzala.
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Kenya nearly added a second in the 70th minute, but substitute Aldrine Kibet struck inches wide.
Uganda grabbed the leveller four minutes later with Abas Kyeyune slotting in the rebound after a Wanzala save.
While Uganda tested their opponents more, the two could not be separated as they settled for a draw after 90 minutes, setting up a further 30 minutes of extra time.
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Just 40 seconds into the extra-time, Uganda completed their comeback through SC Villa youngster Mutebi, who struck past Wanzala following a defensive mix-up.
Owuor nearly grabbed the equalizer for Kenya but goalkeeper Abdu Magada easily saved his weak effort.