Despite the loss, Nigeria finished second in the group with six points from earlier victories over Ghana (4-2) and Togo (3-0), securing qualification for the semi-finals and the 2027 CAF U-20 Africa Cup of Nations in Ghana.
Burkina Faso, who had drawn 1-1 with Ghana and beaten Togo 3-1, topped the group and will face a different opponent in the last four.
The Flying Eagles struggled to break down a well-organised Burkina Faso side and were unable to find the net for the first time in the tournament. The result ends a perfect start for Nigeria but keeps their dual ambitions of a WAFU title and continental qualification firmly intact.
Nigeria will now prepare for a challenging semi-final against hosts Côte d’Ivoire.