Midfielder Bernard Bulbwa scored the winner in the first half.
The win cements Nigeria's place as the successful country in the history of the championship, they now have three more titles than closest rivals Egypt.
Nigeria and the other semi-finalists from the tournament - Senegal, Ghana and Mali - have qualified for the Under-20 World Cup .
The Flying Eagles had already been placed in Group E with Brazil, North Korea and Hungary for the  30 May to 20 June event in New Zealand.
Senegal, Ghana and Mali learned their fate after a draw on Monday,
Ghana are in Group B alongside Argentina, Panama and Austria; Senegal will face Qatar, Colombia and Portugal in Group C; Mali will battle it with Mexico, Uruguay and Serbia in Group D.
Nigeria won a record seventh African Under-20 Championship title by beating hosts Senegal 1-0 in the final on Sunday in Dakar.