Messi's third-minute opener was immediately cancelled out by Ahmed Musa, before the Barcelona playmaker curled a delightful free kick into the top corner.
Nigeria hit back through Musa at the start of the second half, but Argentina earned the three points thanks to Marcos Rojo's goal from inside the six-yard box.
Despite the defeat, Nigeria have progressed through to the last 16 after Iran failed to beat Bosnia-Herzegovina.
Read below to see how the action unfolded in Porto Alegre.
4.01pmHello, and welcome to Sports Mole's coverage of the match between Nigeria and Argentina at the World Cup finals.
4.03pmArgentina have been far from impressive in this tournament but they arrive in Porto Alegre having registered two successive victories to move to the brink of qualification from Group F. They've been reliant on some player called Lionel Messi, though. Not sure if you've heard of him before?
4.06pmIn answer to that last question, of course you have! In truth, Messi has been poor in both his team's previous fixtures but he has delivered two of the goals of the tournament. You can't ask for much more than that, can you?
4.09pmAs for Nigeria, they are the only team in the tournament not to have conceded a goal, which is some achievement. Iran and Bosnia-Herzegovina haven't been the toughest of opposition, but to get through 180 minutes without letting in a goal during a World Cup is impressive. However, they will do well to hold onto that record today!
4.12pmArgentina go into this fixture having already qualified for the last 16 but they still have to work to do to make sure of first place. A draw will be enough, but if Nigeria win this afternoon, they will progress as group winners.
4.16pmIt's a little bit more complicated in Nigeria's case. As I've already mentioned, they will top the standings with a win, while a draw will also be enough for the Super Eagles to take their place in the second round. However, if they lose, things could get interesting. If Nigeria lose and Iran can earn victory over Bosnia, they will have the same number of points. The chances are that it would come down to goal difference, but if Nigeria lose 1-0 and Iran win 1-0, for the first time in World Cup history, lots will be drawn to decide who goes through!
4.18pmAnyway, that's enough of the what ifs, let's crack on with the team news.
4.26pmThe eagle-eyed among you will have noticed that both teams are unchanged from their previous games. In Argentina's case, it's surprisingly because their forward line were disappointing against Iran. Rodrigo Palacio and Ezequiel Lavezzi did well after replacing Sergio Aguero and Gonzalo Higuain, but the latter retain their places in Alejandro Sabella' starting lineup.
4.29pmFor those of you that are interested in following the match between Iran and Bosnia, you can do so by clicking here.
4.32pmWhile I'm on the topic of plugging some of our World Cup coverage, why not head over to our neatly-assembled Stat Centre before we get started in Porto Alegre? Interestingly, Nigeria have the best defence in the tournament but the second worst attack. Could be a fun game...
4.37pmAfter taking a look at Argentina's starting lineup, I can see that the three attackers in Alejandro Sabella's starting lineup - Messi, Aguero and Higuain - have a total of 82 goals between them for their national team. However, they just haven't hit it off in this tournament so far, and the pressure is on for an improved showing ahead of the second round. I don't suppose it matters too much as long as La Albiceleste are winning, but they will face significantly sterner tests in the future. In the event that they lose today, they would find themselves up against France. That would be quite the tussle for a last-16 encounter.
4.41pmAs for Nigeria, the goal-to-game ratio of their attack-minded players doesn't match up to their opponents today, but striker Emmanuel Emenike's record of nine goals in 25 games isn't too shabby. Peter Odemwingie only scores once every six games for his country, but after netting against Bosnia, he should be full of confidence.
4.46pmPREDICTION! On paper, you'd have to say that Argentina should comfortably win this match, but this has been said for their games against Bosnia and Iran too. Sabella would have stressed the importance of a convincing display after criticism in the media and back home, and that could urge Messi and co to produce the goods before the last 16. Argentina to win 3-1.
4.50pmWe've got just 10 minutes to go until kickoff, and the atmosphere is beginning to build at Estadio Beira-Rio. Like in the previous two matches, there is a sea of blue and white but Nigeria, who are likely to get the support of the locals, are well represented too.
4.55pmThe two teams are out and singing their national anthems. There looks plenty of apprehension among the Nigerian players! It's a huge occasion for them. They haven't reached the knockout stages for 16 years.
5 minAnd I was just about to say that it had been a quiet start...
7 minWhere do I start? Argentina took the lead after a shot from Angel di Maria struck the post and rebounded into the path of Lionel Messi, who thumped the ball into the roof of the net from 10 yards. However, a minute later, Nigeria net the equaliser through Ahmed Musa, who curled a stunning effort into the far corner of the net from 16 yards. Sergio Romero had no chance!
10 minCHANCE! It appears as though Messi is "on it" this evening. He slides through an inch-perfect pass to Gonzalo Higuain, who fires marginally wide of the post after taking the ball around Vincent Enyeama.
13 minArgentina have definitely been instructed by their coach that they need to play with a faster tempo. They are all over their opponents in the final third, but so far, the Super Eagles are coping well.
17 minSergio Aguero battles hard on the right byline to earn a corner for his side. The resulting set piece is swung over by Messi, but Enyeama does well to rise above his defence to claim the ball. He's human after all.
21 minEfe Ambrose has just brushed aside Marcos Rojo like he wasn't there, but he couldn't do anything with the ball once he got to the byline. They are doing an effective job in quietening this pro Argentina crowd.
24 minOUCH! Juwon Oshaniwa is down after taking a knee to the back from Fernando Gago. It didn't look intentional, but it must have hurt! In the other game in this group, Bosnia have taken the lead against Iran. That's great news for the Africans.
27 minEmmanuel Emenike is beginning to find some space in between Ezequiel Garay and Federico Fernandez, and his knockdown finds Peter Odemwingie around 30 yards out. However, the Stoke City winger, who has been quiet so far, blasts over.
30 minSHOT! That's a very solid hit from Angel di Maria, who unleashes a 30-yard drive that Vincent Enyeama does well to palm wide for a corner.
32 minArgentina are starting to up the ante again. Sergio Aguero plays a one-two with Manchester City teammate Pablo Zabaleta, but after that move breaks down, the ball rebounds to the striker, who sees his 12-yard strike blocked by a Nigerian defender.
37 minSUBSTITUTION! This is a blow for Argentina. Sergio Aguero, who had slowly began to feature in this match, is coming off with what could be a tournament-ending injury to be replaced by Ezequiel Lavezzi.
39 minArgentina go straight back up the other end and earn a corner after a Marcos Rojo cross was deflected wide. The set piece was headed on goal by Federico Fernandez, but Vincent Enyeama opted for safety first and palmed the ball over.
42 minA wall of green shirts have formed a blockade on their 18-yard line as Argentina press for a second goal before half time. Lionel Messi and Angel di Maria are looking particularly lively, but so far, they can't find a way through.
44 minSHOT! What an effort! There appears to be no danger when Argentina win a free kick from around 35 yards out, but Messi produces the most accurate of attempts that forces Vincent Enyeama to claw the ball from the top corner.
45+1 minTurns out that earlier effort was just his warm-up effort! That's quite sensational from Lionel Messi, who curls a 20-yard free kick into the top corner. Vincent Enyeama had no chance. And that's your lot for half time!
5.51pmThe half-time whistle goes at Porto Alegre, and Argentina hold a 2-1 advantage over Nigeria. It's been Lionel Messi's half - how many times have we said that before?
5.54pmNigeria have played their part in what was a competitive first 45 minutes, but the statistics suggest otherwise. Argentina have had 70% possession, had seven shots on targets and created six corners compared to none from their opponents. This isn't over, though. Nigeria have shown enough quality in the final third to suggest that they can net another goal in this match.
6.03pmThe two team are making their way back out for the second half. As it stands, both of these teams are heading through. For that to change, Iran will need to come from behind to beat Bosnia.
47 minHello! We have a World Cup classic on our hands. The Argentina defence is calved open and Ahmed Musa has plenty of time to pick his spot and curled the ball into the corner from 12 yards. Remember, if Nigeria win this game, they top the group!
50 minAnd we all thought this wasn't going to be an entertaing game...! Argentina go straight up the other end, earn a corner, and score. Simple as that. Ezequiel Lavezzi's delivery found Marcos Rojo, who diverted the ball into the corner with his knee for his first international goal.
55 minLionel Messi has had the ball on a piece of string today. He turns away from his marker with such speed before sliding the ball in for Gonzalo Higuain, but the Napoli forward sees his shot turned away by Vincent Enyeama.
58 minGonzalo Higuain has been much improved from his showing against Iran and he does well to win a corner off Joseph Yobo. However, the corner into the box is poor and Nigeria are able to clear. For those of you that are interested, it is still 1-0 to Bosnia in the other game.
60 minActually, I tell a lie - Miralem Pjanic has scored for Bosnia! That should be enough to confirm Nigeria's place in the second round.
62 minSUBSTITUTION! Lionel Messi is being withdrawn by Argentina, and the reception that he is getting is incredible. The Argentina faithful salute their hero and applaud Ricardo Alvarez onto the pitch.
64 minSUBSTITUTION! While that substitution was taking place, our attention was drawn to Michel Babatunde, who is in some trouble on the ground. He could have a broken arm after getting in the way of a shot from one of his own players.
68 minWith the pressure off both sides, the match is beginning to open up a bit. Nigeria know they are almost through so are prepared to push a few men further forward, but they are finding themselves left open to the counter-attack. Neither team are able to test their opponent's goalkeeper.
72 minAfter the injury to Sergio Aguero, Ezequiel Lavezzi will feel as though he has the chance to prove himself ahead of the second round, and he displays his qualities by accelerating past two defenders before sending a teasing cross into the middle. However, no-one is able to provide the finishing touch.
74 minCHANCE! Ahmed Musa gets close to his hat-trick! A cross from the right was powerfully drilled into the centre where Musa sent a first-time volley over the crossbar under pressure from Pablo Zabaleta.
78 minSAVE! Beautiful, beautiful play from Argentina. Ezequiel Lavezzi touches the ball to Angel di Maria before advancing into the penalrta. Di Maria waits before scooping the ball into the path of the Paris Saint-Germain man who takes the ball first time, but Vincent Enyeama is equal to it.
82 minArgentina had been starting to assert themselves but Nigeria are coming back into this. The likes of Garay and Fernandez have had to put there bodies on the line to prevent shots getting through to Romero's goal. There's still eight minutes to go.
84 minSHOT! Emmanuel Emenike tries his luck from a considerable distance out, but his strike is always swerving away from goal and Sergio Romero can watch it fly past the post. The other game is now 3-1 to Bosnia, but it won't influence who goes through to the last 16.
87 minCHANCE! Nigeria go close again and Alejandro Sabella isn't a happy chappy! Efe Ambrose powered his way inside from the right before seeing his shot deflected into the side-netting.
90 minThere will be four minutes of added-on time.
90+3 minSHOT! Angel di Maria attempts to catch Vincent Enyeama off his line from the halfway line, but the ball clears the crossbar by a matter of inches. That ought to be it as far as chances are concerned.
6.55pmThe full-time whistle has gone in Porto Alegre and Argentina have secured their place at the top of Group F with a 3-2 victory over Nigeria, who also make it through to the last 16.
6.58pmLionel Messi will deservedly take the plaudits, but credit should also go to Nigeria, who made this match a lot more competitive than a lot of people, including myself, thought it would be. They are likely to have France in the last 16, while Argentina will play Ecuador or Switzerland.
7.01pmThat will be all from Sports Mole's coverage of this match. Thank you for joining us for this game, and we hope to see you again later for the conclusion of Group E. Goodbye for now.