Croatia advance as winners of Group D with the maximum nine points after beating Iceland 2-1 and Nigeria were just minutes away from joining them before central defender Rojo superbly volleyed home a Gabriel Mercado cross from the right.
Messi had put Argentina ahead in the 14th minute, with a fabulously taken goal but the Africans equalised through a Victor Moses penalty in the 51st minute and the twice World Cup winners struggled to respond to that setback with a ragged second half display.