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.
Syphas Owuor had given Kenya the lead in the second half before Uganda fought back to victory.
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.
Kenya nearly added a second in the 70th minute, but substitute Aldrine Kibet struck inches wide.
Uganda grabbed the leveler 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.
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.