The Young Cranes will face Ghana, the most successful country in the country in the final next Saturday.
In the earlier semifinal match Ghana had edged fellow West Africans Gambia thanks to a thumping freekick by Percious Boah after thirty minutes.
The Young Scorpions had beaten Ghana in their final group game to earn a place in the knockout stage.
Uganda will go into Saturday's final against Ghana as underdogs given the West African nation's pedigree in the competition they had won on three previous occasions.
They will have to rely heavily on their talisman striker Derrick Kakooza who has the distinction of scoring the tournament's only hat-trick so far.
Tunisia will face Gambia in the fight for third place.
The Under-20 Nations Cup was previously used as a qualifier for the World Cup but due to the coronavirus pandemic, the global competition that would have taken place in Indonesia later this year will no longer hold as planned.