The Barcelona forward lashed a rebound high into the net on three minutes before notching his fourth goal in three matches with a wonderful free kick as La Albiceleste maintained their 100 per cent record.
Nigeria, who have also qualified for the knockout stage for the first time since 1998 thanks to Iran's defeat, had pulled level within seconds of Messi's opener when Ahmed Musa cut in from the left and curled a delightful effort into the far corner.
And the CSKA Moscow forward was at it again just a few moments after the break when he glided onto a clever through pass and coolly steered into the corner.
But Argentina weren't to be denied and ensured top spot by immediately restoring their lead when Marcos Rojo diverted a left-wing corner in off his knee.
PRE-MATCH: Familiar faces. Argentina are unchanged from the last-gasp win over Iran with Messi, Aguero and Higuain leading the attack as part of a 4-3-3 formation. Nigeria also stick with the starting XI that edged past Bosnia. Stoke forward Peter Odemwingie, who struck the only goal of that game, will play on the right of a supporting three behind Fenerbahce striker Emmanuel Emenike. Ex-Everton defender Joseph Yobo wins his 100th cap for the Super Eagles.
3' - GOAL! Argentina 1-0 Nigeria. Messi!!!! It's 3 in 3. Di Maria races onto Mascherano's ball and hammers a shot at goal that ricochets off the post and keeper before falling to Messi who lashes it into the roof of the net.
4' - GOAL! Argentina 1-1 Nigeria. What a start! Nigeria are level immediately. Ahmed Musa races into the left side of the area, cuts inside and curls a beauty into the corner. 1-1 inside four minutes!
9' - ARGENTINA CHANCE! Argentina come again and Messi slips a sensational pass through to Higuain who rounds the keeper but fires into the side netting from a tight angle.
30' - ARGENTINA CHANCE! Di Maria takes a pass from Messi and moves it out of his stride before unleashing a low drive that Enyeama is forced to get down and tip past his left-hand post.
44' - ARGENTINA CHANCE! Messi steps up and curls in a delicious effort that arrows towards the top corner before Enyeama intervenes to tip it over.
45+1' - GOAL! Argentina 2-1 Nigeria. Messi does it again! A sublime curling free kick whips over the wall and into the left-hand corner of Enyeama's net.
48' - GOAL! Argentina 2-2 Nigeria. Messi 2-2 Musa.... Musa grabs his second of the game and we are all square. The forward latches onto Emenike's pass and coolly tucks it home.
50' - GOAL! Argentina 3-2 Nigeria. Argentina regain the lead. A corner from the left is missed at the near post and Rojo arrives to divert home via his knee.
80' - NIGERIA CHANCE! Musa leads a super break, the forward cuts in from the left and looks set to drill in a hat-trick before Zabaleta recovers with the block-tackle of the match.
Nigeria have lost all four World Cup meetings with Argentina.
Messi is the second Argentinean to score in all 3 (first phase) group matches after Orestes Omar Corbatta in 1958.
Joseph Yobo earned his 100th international cap and became the first Nigerian to achieve the feat.
Argentina have won 12 of their last 15 World Cup group games.
They have won five of six World Cup games against African opposition. Their only defeat was their first match in that sequence, a 1-0 loss to Cameron in 1990.
(Stats courtesy of Opta)
Is Messi edging close to being crowned the greatest ever! It's been a heated debate over the past few years as to whether Messi's incredible feats with Barcelona are enough to see him eclipse Pele and Diego Maradona as the best footballer of all-time. His critics claim he needs to 'own' a World Cup to truly compare; well he's getting close. Four goals in three matches have seen him make a great start and if he goes on to help Argentina claim another world crown, the arguments against him will be few and far between.
MAN OF THE MATCH
Lionel Messi (Argentina): Lively, inventive and looking close to his best. The diminutive attacker almost had his spotlight stolen by Musa - almost. Two sensational goals and an all-action display suggest the best could still be to come from the Barcelona star.
Argentina: Romero 6, Garay 6, Zabaleta 7, Rojo 7, Fernandez 6, Gago 7, Mascherano 6, Di Maria 8, Messi 9, Aguero 6, Higuain 7. Subs: Lavezzi 6, Alvarez 6, Biglia n/a.
Nigeria: Enyeama 7, Yobo 6, Ambrose 6, Mikel 6, Oshaniwa 6, Onazi 6, Babatunde 6, Omeruo 6, Odemwingie 7, Musa 8, Emenike 6. Subs: Uchebo 6, Nwofor 5.
MATCH IN A TWEET
- Sports & Recreation
- Lionel Messi
- Ahmed Musa
- Joseph Yobo