The encounter saw Nigeria and South Africa, who lost out to Mali and Senegal respectively in the semis eager to take something home from the tournament during the losers final at the Stade General Seyni Kountchey Stadium which ended goalless after the end of 90 minutes.
The Paul Aigbogun tutored-Flying Eagles paraded youngsters who have tasted little or no action like Detan Ogundare who replaced first choice Orewale Oredale in goal, alongside the likes of Peter Eletu, Solomon Ogberahwe and Paschal Onyekachi were on the front-foot at the start of the contest, but their efforts yielded no dividend.
In the 11th minute Nigeria missed a decent chance to score off Jamil Muhammad shot that missed target.
The pair of Onyekachi and Maxwell Effiom also failed to convert glaring chances in the first stanza.
South Africa's winger Kobamelo Kodisang missed a sitter after he failed to net as the opportunity failed to hit target.
In the second stanza, Yahaya Nazifi was close to net the opener for Nigeria after coming off the subs came bench, but after beating South Africa's shot-stepper, Kuhbeka his effort could not find the back of the net.
At the end of regulation time with nothing separating both teams, the dreaded penalty-shoot-out was employed to decide the contest.
Ibrahim Alhassan's miss from the spot to ensure Nigeria could only settle for fourth place, and a ticket to fly the continent's flag at the FIFA U-20 World Cup later in the year.