The Super Eagles were on Monday pegged 2-1 by 2026 World Cup qualifying rivals Rwanda in a final 2025 AFCON qualifier in Uyo.
It was the first win by Rwanda over Nigeria at full international level.
Despite the disappointing home loss, the Super Eagles won Group D with 11 points from six matches.
Rwanda finished on eight points, but failed to qualify after Benin held hosts Libya to a goalless draw in Tripoli to go through to Morocco 2025 on better goals difference.
The Super Eagles opened scoring in the 59th minute courtesy of the individual brilliance of substitute Samuel Chukwueze.
He simply raced the heart of the crowded Rwanda defence before he delivered a low shot that beat the goalkeeper Fiacre Ntwari.
However, Rwanda drew level in the 72nd minute, when Jummy Mutsinzi headed home a header beyond goalkeeper Maduka Okoye.
The visitors then pulled ahead three minutes later through Innocent Nshuti.
In the 50th minute, a header by Victor Boniface off Moses Simon corner was saved by the outstanding Rwanda goalkeeper, who was Man of the Match when both teams played out a scoreless draw in Kigali in September.
It was a tepid first half with the only clear chance falling to Kelechi Iheanacho, but his left-footed strike was kept out by the Rwanda shot stopper.
Super Eagles Starting XI vs Rwanda(4-3-3) Maduka Okoye – Bright Osayi-Samuel, William Ekong (Captain), Gabriel Osho, Bruno Onyemaechi – Raphael Onyedika, Alhassan Yusuf (Frank Onyeka 46), Fisayo Dele Bashiru (Osimhen 77) – Moses Simon, Victor Boniface (sadiq Umar 88), Kelechi Iheanacho (Samuel Chukwueze 46)
