After some neat footwork, the striker turned and smashed home a wonderful effort for his first World Cup goal.
Argentina continued to press but Messi was subdued in the face of muscular Icelandic defence and the teams went into the break on even terms.
Messi has missed more than 20 penalty kicks in his career, showing there is perhaps one flaw in his genius.
Iceland then had the best chance of the rest of the half, as Gylfi Sigurdsson had low shot parried away from close range, though Caballero was again guilty of pushing the ball back into the danger zone rather than away from the goal.
VAR has been used to varying degrees of success in Serie A and the German Bundesliga, while Federation Internationale de Football Association used the system at the Confederations Cup in Russia a year ago.
The small Nordic island nation's team could have taken an early lead today but Birkir Bjarnason side-footed a shot wide of goal when goalkeeper Willy Caballero was exposed. And when presented with a penalty opportunity of his own, he contrived to put it at the flawless height for goalkeeper Hannes Halldorsson to parry away.
At least Messi's miss in the 64th minute at Spartak Stadium - his fourth in his last seven penalty attempts for his club and his country - was not in a losing cause.
"Physically Iceland are very strong, but now we must only think about what is ahead".
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But Argentina fans should absolutely be concerned that Messi isn't just in Ronaldo's shadow at this tournament. In the final minute, Ronaldo had whipped in a free kick to equalize for Portugal against Spain; Messi, presented with a similar set play, his third of the game, scuffed his shot into the wall. Iceland's defense was resilient for a while but eventually they were broken through with Sergio Aguero being able to turn in the box and finish emphatically for the opener.
Sampaoli saw his midfield gamble wasn't working and quickly introduced Ever Banega in the second half to add more creativity and lessen the burden on Messi.
"Croatia are a great team and Nigeria are also good".
It might also be pointed out that when Iceland drew 1-1 with Portugal at Euro 2016, Ronaldo had 10 shots and did not score; here Messi had 11 and also did not score. Halldorsson said to a reporter who asked why Iceland celebrated so much for a draw.
Croatia beat Nigeria 2-0 on Saturday with an own goal from Oghenekaro Etebo and a penalty from Luka Modric to go top of World Cup Group D, one of the toughest and most unpredictable in the tournament.
However, Heimir Hallgrimsson's side was undeterred by the setback of conceding first.
Halldorsson made another good stop to claw away Pavon's risky cross and Iceland replaced goal scorer Finnbogason with Bjorn Sigurdarson and they held on despite Messi firing narrowly over in stoppage time.
"We do not have to go insane, we deserved to win, but we have to improve a lot, now we have to be calm".