The offence occurred in the first-round, second-leg match against Rwanda, which Uganda won 2-1 to secure a 3-2 aggregate victory.
However, Uganda's Aheebwa James had different dates of birth on his passport and his inter-clubs licence.
Rwanda have been reinstated and will take on Egypt in the second round.
The Rwandan Football Federation had challenged the eligibility of Tumwesigye Frank, Aheebwa James, Lwalirwa Halid and Kizza Martin.
Only James was found to have different birth dates: 19/5/1998 on the passport, and 27/3/1997 on his Confederation of African Football Inter-clubs licence.
Although both dates place James within the age limit for the competition, the rules state that both dates must match.

Trinity chairman Michael Carter said in Sunday's Salford programme notes that 2017 is their final year at Belle Vue.
The venue would not meet minimum ground standards for the top flight.
"We believe Wakefield playing at Featherstone would be the best-possible fit for supporters," Rovers general manager Davide Longo said.
"[Particularly] given the fact our stadium is situated less than five miles away."
Longo said informal talks had been held between the clubs which, if successful, would see Trinity play home fixtures in the town in addition to their existing training agreement.
"I think it goes without saying that our stadium meets minimum standards set by the Rugby Football League," he added. "And we are constantly making improvements to ensure it continues to develop as a high-quality facility - fit for top-flight and even international rugby league.
"I, for one, sympathise a great deal with the Wakefield board of directors, staff, players and supporters, given the predicament they find themselves in. "
It is not the first time Wakefield have considered moving on - with Dewsbury tipped as a destination - before an agreement to redevelop the site was completed.
However, there has been no further development six months on and Trinity, who moved into the ground in 1895, have issued notice of their intentions to leave.
Super League's minimum requirements for 2016 stipulate that grounds must have a minimum capacity of 5,000, with 2,000 of that seated.
Belle Vue's capacity is just over 7,000 while Post Office Road has an 8,000 capacity.
There are other requirements including media facilities, disabled access and provision as well as closed-circuit television and parking.
Uganda have been disqualified from qualifying for the 2017 Under-20 Africa Cup of Nations for fielding an ineligible player.
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Featherstone Rovers have made a formal offer to Super League club Wakefield Trinity to ground-share at Post Office Road for at least 2018.