With only a point in two games, the Argentines needed to defeat the Super Eagles for a chance to qualify for the knockout stage of the competition.
Messi’s opener was cancelled out by Victor Moses’ strike from the penalty spot before Marcos Rojo’s 86th-minute effort secured a 2-1 victory over Gernot Rohr’s men.
Argentina were later eliminated in the Round of 16 by France, who went on to win the tournament.
Reflecting on his side’s performance in the tournament, the five-time Ballon d'Or winner admitted that their poor preparation led to their below-par display in the global showpiece.
"When we lost and crashed out of the tournament, we knew our time was up because our preparation and focus towards the tournament was not too impressive,” Messi told Fox Sports Radio in Argentina.
“It would have been very humiliating if Nigeria had eliminated us at the group stage.
"The World Cup in Russia was a complicated period for us. But people knew we were not candidates to win. Today is different, I see a young and excited group ready for success.
"When we qualified against Nigeria in the World Cup everyone who was mocking us was silent, they wanted us to be humiliated. If we were knocked out in the groups they would have killed us all.”
The Super Eagles will be looking to put behind them their disappointing early exit from the World Cup in Russia by challenging for glory in the 2019 Africa Cup of Nations in Egypt, starting on June 21
The three-time African champions have been drawn in Group B along with Burundi, Guinea and Madagascar.