The Falconets suffered a 2-1 defeat to the Scorchers in Saturday’s second-leg encounter but advanced 3-2 on aggregate, having secured a 2-0 victory in the first leg played in Ikenne.
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Faith Chimzimu scored twice for Malawi in the ninth and 56th minutes to wipe out Nigeria’s first-leg advantage.
However, Christopher Precious restored Nigeria’s lead in the 62nd minute with a crucial goal that ultimately sealed qualification for the Moses Aduku-led side.
The tournament appearance will mark Nigeria’s 12th participation since the competition debuted in Canada in 2002.