The few Nigerian fans in the crowd also left happy because their team advanced to the knockout phase thanks to Bosnia's 3-1 win over Iran. Argentina finished on nine points, Nigeria on four, Bosnia three and Iran one.
The match at Beira Rio stadium was as close as Argentina will come to a home game at this World Cup as an estimated 150,000 fans flooded across the border into this southern port city looking to get in on the party and Messi made sure it started early with a fabulous strike in the third minute.
While some questions continue to hang over Argentina's status has one of the tournament favourites, Messi's performance through the group phase of the competition has been nothing short of sensational impressing fans, team mates, coaches and opponents.
"Messi is one heck of a player, you can’t take it away from him," Nigeria coach Stephen Keshi told reporters after Nigeria became the first African team to reach the last 16 in this tournament. "There are good calibre players in the Argentina team but Messi is from Jupiter."
Although Argentina were guaranteed a place in the last 16, the twice champions still had plenty to play for on a drizzly day with top spot up for grabs and the soccer world waiting for the Sky Blues to flash their championship credentials after uninspiring wins over debutants Bosnia and unfancied Iran.
"It's beautiful to see so many Argentine fans, I think we saw a very good Argentine team," said Messi, after bringing his World Cup tally to four putting him level with Brazilian Neymar at the top of the list of leading scorers. "We want more.
"We had said we strikers were perhaps a little still and were not finding spaces. Now we corrected that.
"We continue in the search of the dream we all want."
Nigeria entered the contest as the only team who had yet to concede a goal but had not faced a side with the attacking quality of Argentina, who immediately put the Super Eagles under pressure.
Boasting one of the most intimidating attacking formations in the business with Messi, Sergio Aguero, Gonzalo Higuain and Angel Di Maria, Argentina had managed just three goals in two matches.
But the "Fab Four" were on song against Nigeria, with a dominating attacking display led by Messi, who struck twice in the opening half and looked dangerous throughout.
FREE KICK
Messi, who celebrated his 27th birthday on Tuesday, lashed in a rebound to give his side the lead after three minutes and scored again in first-half stoppage-time when he curled a sensational 20-metre free kick into the corner of the net.
Argentina's brilliance on the attack was offset by shaky defence as Nigeria's Ahmed Musa twice cancelled out Messi goals with neat finishes in the fourth and 47th minutes.
The Argentine crowd was stunned when Musa scored just after halftime but were quickly back on their feet celebrating three minutes later when a charging Marcos Rojo stabbed home a bouncing ball with his knee from close range.
"We started improving from the point of view of structure. We see an improvement as a whole," Argentina coach Alejandro Sabella told reporters. "You can win not playing well and still have things to correct, I’m pleased about the nine points but I must always improve."
Argentina will play the Group E runners-up, likely to be Ecuador or Switzerland, in the last 16 while Nigeria will probably face France.
(Editing by Ed Osmond and Nigel Hunt)
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