Messi opened the scoring after just three minutes, slamming the loose ball into the roof of the net as Angel Di Maria’s strike rebounded into his path before he added his second of the evening just before half-time with a stunning free-kick.
Ahmed Musa twice pegged Argentina back with two well-taken efforts, but Marcos Rojo bundled home a third from close range to seal the three points and top spot for Argentina.
Sabella’s men had failed to truly convince in their previous wins over Bosnia and Iran, but the former Sheffield United and Leeds midfielder thinks they are heading in the right direction after a tough test in Porto Alegre.
"Nigeria are a versatile team, but they were not as aggressive when they occupy the spaces," said Sabella.
"We started improving from the point of view of structure. We see an improvement as a whole. I don't like speaking about individuals.
"The strikers played a better game this time. The weakness we discuss at home in private.
"You can win not playing well and still have things to correct, I'm pleased about the nine points but I must always improve."