The Super Eagles were heading through to the last 16 at Argentina's expense with four minutes to go of the final Group D game, but Rojo's sensational low volley saved Jorge Sampaoli's men.
Lionel Messi gave Argentina the lead in St Petersburg on Wednesday morning (AEST), the Barcelona superstar scoring a stunner to bring up the 100th goal of Russia 2018.
But when Javier Mascherano dragged down Leon Balogun in the box shortly after the restart, Victor Moses stepped up to roll Nigeria level and within touching distance of progressing.
Sampaoli sent on attackers Cristian Pavon, Maximiliano Meza and Sergio Aguero, but it was defender Rojo who came up with a quite brilliant winner.
The right-wing cross from another defender, Gabriel Mercado, was perfectly placed for Rojo to arrive late and slam home an improbable, unstoppable finish that extends Argentina's stay at the World Cup.
