The game appeared to be heading to a scoreless draw but the Genk striker towered above his marker to head home three minutes into stoppage time after an initial shot from Victor Osimhen was blocked.
The Super Eagles had already booked their place at the tournament earlier in the day after Sierra Leone could not salvage a win against Lesotho.
Benin goalkeeper Saturnin Allagbé thrice denied the trio of Kelechi Ihenacho, Henry Onyekuru and Osimhen.
The Benin side grew into the game in the second half after playing conservatively in the first stanza before the back-breaking goal.
Nigeria have an unassailable lead at the top of the table with 11 points garnered after five matches and will top Group L of Africa Cup of Nations qualifying regardless of what happens in their final match against Lesotho on March 30.
Izuchukwu Okosi
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