Uganda attacking midfielder Travis Mutyaba would then take matters to his own hands despite the over 15,000 Kenyan fans singing louder for Junior Stars, troubling the Kenyan defense with quick runs.
Mutyaba forced four consecutive fouls in the 30 yards from goal on opposite ends, a move that troubled Kenyan coach Salim Babu standing on the touch line.
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The Ugandan physical style of play proved too much for Junior Stars in the midfield, forcing Babu to introduce Spain-based Aldrine Kibet and Lucas Kungu in place of Elly Owande and Humphrey Aroko. Kibet went on to win the golden boot award with three goals.
The change made five minutes to half time improved Kenya's attack as Louise Ingavi blasted Kenya's first real chance wide after being released through with a looping header from Syphas Owuor.
Ugandan winger then Richard Okello got the ball inside the net but it would be ruled out for offside as the two sides went to the break tied at 0-0.
Omalla almost scored the winner in the 93rd minute but his effort went inches wide after receiving a long free kick delivery from Stanley Omondi as the game headed to extra time.
After being silenced in the second half, Mutyaba returned to haunt Kenya, this time with a goal, sending the ball into an empty net after a goalmouth melee gifted him the loose ball to give Uganda a 2-1 lead.
The Ugandans held on to their slender lead to win the Cecafa title.