Alejandro Sabella's side were frustrated by superbly resilient opposition until the Barcelona star bent home a fantastic goal in second-half injury time
Few would have expected Argentina, viewed as one of the favourites to win the tournament, to be given too much of a test by a team that has never gone beyond the first round of a World Cup in three previous appearances.
However, Carlos Queiroz's side, who had been criticised for their defensive style of play following their opening Group F goalless stalemate against Nigeria, produced another resolute display at Estadio Mineirao on Saturday to come within a few minutes of a highly creditable draw.
But, in injury time, it was Messi who stepped up when it mattered most, curling home brilliantly into the corner to give the South Americans a place in the last 16.
Meanwhile, Iran will head into their final group game with Bosnia-Herzegovina on Wednesday reflecting on an opportunity missed, and knowing that only victory will be enough to extend their tournament.
Argentina unsurprisingly dictated the opening stages without creating any clear-cut opportunities against an Iran defence that displayed the same determination as against Nigeria.
Gonzalo Higuain was the first to test the Iran backline after 13 minutes, but goalkeeper Alireza Haghigi showed quick reactions to race out and block the Napoli striker's effort after he had been played through by Fernando Gago.
Higuain was involved again as he linked up with Sergio Aguero inside the area, only to see the Manchester City man's curling effort brilliantly kept out by a fine diving save from Haghigi.
Aguero then headed wide from a corner as Argentina's dominance of play continued, yet Iran, with impressive commitment and organisation, did not have too much difficulty in keeping the South Americans at bay.
Iran's ability to maintain parity also owed much to Argentina's profligacy, which was demonstrated in the 35th minute when defender Ezequiel Garay headed a Messi free kick over the crossbar.
Queiroz's men were able to fashion some first-half opportunities of their own, the best of which came after 41 minutes as centre-back Jalal Hosseini turned Ashkan Dejagah's corner narrowly wide of the post.
Pablo Zabaleta went close from the edge of the area in the opening stages of the second half, but it was Iran who continued to look more threatening.
Indeed, they would have taken the lead in the 53rd minute had forward Reza Ghoochannejhad not directed his header straight at Argentina goalkeeper Sergio Romero following a fine break.
Iran felt they should have been awarded a penalty a minute later after Zabaleta appeared to bring down Dejagah, with replays suggesting that the South Americans had been given a let-off.
At the other end, Messi failed to find a finish after surging forward with an archetypal run from midfield and curling wide of the post.
With time running out, Romero was called into action to tip Dejagah's header over and Iran had an even better chance when Ghoochannejhad was sent clear one-on-one but saw his somewhat tired finish parried.
But just as they looked set to celebrate their famous point, Messi struck.
The Barcelona man worked space on the edge of the area before opening his body to bend a shot into the corner, as Argentina's class – and more accurately that of their captain – finally told.