El Kun had levelled the former Parma and Inter striker with the winner against Russia in Saturday's friendly.
And the Manchester City man now has only Lionel Messi and Gabriel Batistuta ahead of him as he found the net once more in Krasnodar.
Aguero was on hand to slot home from close range after fine work from Cristian Pavon out wide had stretched the Nigeria defence.
GOAL! @aguerosergiokun finishes off a swift counter to double @afa 's lead.
SIGN UP & WATCH ON fuboTV → https://t.co/zNDaRUbJFg #beINfuboTV pic.twitter.com/pMrpVETq2I — beIN SPORTS USA (@beINSPORTSUSA) 14 de noviembre de 2017
That strike put Argentina 2-0 up, after Ever Banega had earlier capitalised on a bizarre error from Daniel Akpeyi by firing home a free-kick after the goalkeeper inexplicably picked the ball up outside his area.
Kelechi Iheanacho later narrowed the deficit with a fine set-piece of his own on the stroke of half time.
Aguero now has 36 goals for the Albiceleste, and with two in his last two appearances, the City star is strengthening his claim to start at next year's World Cup as the first-choice centre-forward.
Messi lies in front as Argentina's all-time best marksman with 61 goals, with Batistuta in second spot having smashed 54 in his 77 international appearances.
Curiously, Kun has never netted at a World Cup finals - a record he will be desperate to set straight next year in Russia as Argentina look to go one better than the runners-up spot managed at Brazil 2014.