Argentina needed to save face after the loss to Croatia, and showed their intentions with the first shot from Nicola Tagliafico.
Ahmed Musa, the record goal-scorer at the finals for Nigeria, replied with a shot on the turf that rolled into the loud Saint Petersburg crowd.
La Albiceleste had the first joy as Lionel Messi controlled brilliantly from an Ever Banega pass to dispatch emphatically on 14 minutes.
From scoring, Messi nearly turned provider to the returning Gonzalo Higuain, but brave goalkeeping from Francis Uzoho kept the Juventus man off bounds.
Messi came to the party in a big way when he almost put more pain in Nigerian hearts, with his curling free-kick striking the post with the help of Uzoho's fingertips.
From the restart, the West Africans made the first change with Kelechi Iheanacho recalled for Odion Ighalo.
The Super Eagles were set to draw level when they earned a penalty after a foul by Javier Mascherano on Leon Balogun.
Victor Moses coolly converted from 12-yards, sending debutant Franco Armani the wrong way after 51 minutes.
Staring elimination and under pressure, Argentina made a tactical switch as Cristian Pavon entered for Enzo Perez.
The Nigerians were buoyed in confidence and Wilfred Ndidi's ominous attempt from range worried the opposing side as it just sailed over the top.
With eight minutes to go, Ighalo was left unmarked and ran towards goal with a clear sight but Armani pulled off a good save.
The two-time World champions made them pay when Manchester United’s Marcos Rojo showed a striker’s instinct with a first-time volley after a delightful cross from Gabriel Mercado to break Nigerian hearts.
Nigeria XI: Uzoho, Idowu, Ndidi, Ekong, Balogun, Musa, Etebo, Mikel, Moses, Iheanacho, Omeruo
Argentina XI: Armani, Mercado, Tagliafico, Banega, Higuaín, Messi, Di María, Mascherano, Pérez, Marcos Rojo, Otamendi