Uche Nwofor bagged his third goal of the tournament in the first half, and Stanley Okoro claimed his second with a penalty on the stroke of full time, after Kayode Olanrewaju was felled in the box.
A grim performance, littered with stray passing, ended in a 1-0 defeat to Cameroon in their second group game of the campaign.
A 2-0 defeat of Gambia sealed qualification without being convincing, but the same cannot be said of the semifinal triumph over Group A winners Mali.
The Flying Eagles never looked in danger of conceding from the Malians, who only mustered one effort in target in 90 minutes.
And when Nwofor tapped in from close range after just 22 minutes, the encounter looked done and dusted. Nwofor could have added a second with the last kick of the half, but was denied by goalkeeper Sy's exceptional save.
Mali hugged possession in the second period, but found the Nigeria defence unyielding.
Their fate was finally sealed when Olanrewaju forced his way into the box, to be scythes down by the desperate Diallo.
Okoro, on as an 89th minute substitute, had had enough of a feel for the ball to stroke it confidently past Sy.
The Nigerians will now await the winners of the second semifinal between Cameroon and Egypt.
CLICK HERE for the AYC news and results.