The super eagles produced a stunning display to dispatch the Albiceleste 4-2 in Krasnodar.
Argentina were two goals up through Ever Banega and Sergio Aguero when Nigeria started their comeback.
Arsenal forward Alex Iwobi scored twice as Nigeria comfortably overcame the challenge of Argentina.
Sergio Aguero moved clear in third place on Argentina’s all-time scoring list before Jorge Sampaoli’s side fell apart in the second half.
Sergio Aguero scored his 36th international goal to move clear in third place on Argentina’s all-time scoring list as Jorge Sampaoli’s side looked set to prosper despite the absence of Messi, who had returned to Barcelona after featuring in the 1-0 win over Russia on Saturday.
Having drawn level with Hernan Crespo by scoring a late winner against the Russians, Aguero followed up his first international goal since June 2016 by tapping home Argentina’s second to back up Ever Banega’s free-kick opener.
Yet their comfortable cushion evaporated either side of the interval.
Kelechi Iheanacho pulled one back inspiring a Nigeria fight back with a free-kick of his own in the closing stages of the first half.
Two goals in the space of three second-half minutes from Iwobi and Bryan Idowu swung the game further away from Argentina.
Iwobi then slot home a fourth to secure Nigeria just their second ever win over their South American opponents.