Nigeria ended Benin Republic's eight-year unbeaten run at home, when they completed the double over their West African rivals, in the 2022 Africa Cup of Nations qualifying series.
Paul Onuachu's late header clinched a 1-0 win in Porto Novo on Saturday.
The Super Eagles had come from a goal down last year to beat the Squirrels 2-1.
However, away from home, Gernot Rohr's men found it tough, until the final moments of the game.
The three-time African champions had already qualified for the tournament before kick-off, thanks to Lesotho's goalless draw with Sierra Leone earlier in the day.
With one round of fixtures left, Nigeria lead Group L with 11 points, four more than Benin.
Sierra Leone have four points, while Lesotho are bottom with three.
The Eagles host Lesotho in their final fixture on Tuesday.
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