Messi, cheered by fans with his every touch, set up Gonzalo Higuain for the opening goal after 24 minutes and it was from his mesmerising run and shot that Angel Di Maria doubled the lead two minutes later.
Nigeria pulled one back through substitute Chinedu Obasi soon after the restart but an own goal from Elderson midway through the half restored Argentina's two-goal cushion.
"He [Messi] did not score but he assisted in all three goals. He was the best player in the match. It does not matter whether he scores of not," Argentina coach Alejandro Sabela told reporters.
"Nigeria have some very fast strikers so I had to be a bit extra cautious putting an additional defender in the line-up. But our midfield made all the difference with Messi providing some good passes."
A strong Argentina side then went in front thanks to Messi's astute chipped past that found an unmarked Higuain and he fired home.
Argentina's second soon after owed much to a brilliant jinking run by Messi who beat three defenders before seeing his curling shot saved by Dele Aiyegnuba. The keeper was powerless though from stopping Di Maria tapping in the rebound.
"It was so obvious that Messi did make the difference," said Siasia.
"We tried our best to stop him but you know he is the world's best player. Whenever he gets the ball he made a problem for us."
