The South Americans, two-time world champions, seemed destined for an early flight home until they found an unlikely hero in the guise of Manchester United defender Marcos Rojo.
His superb volley in the 86th minute earned Argentina a 2-1 win in St Petersburg and sent them through to a last-16 tie against France, ending a tumultuous group stage which saw fallouts, huge criticism, constant changes of formation and even questions over who was picking the team.
But what now for Argentina? Can they put their problems to one side and be a force for the rest of the tournament?
A huge relief for all of us - Messi
The Argentine camp had been the subject of numerous stories and rumours ever since the disastrous 3-0 defeat by Croatia, with the team called "the worst ever" and Sampaoli begging fans for forgiveness.
A change to a back four brought about a much-improved first-half display, and they led at the break through Messi's expertly taken goal.
Victor Moses' second-half penalty threatened to derail that improvement, but Rojo's late strike earned Argentina passage into the last 16.
"It was a difficult situation," said Messi, who was pictured giving a team talk in the tunnel before the players came back out for the second half.
"It was a huge release and relief for all of us. It is a huge joy for everyone for the difficult days we lived after the last defeat. Luckily we achieved our objective."
Sampaoli was embraced by Messi at full-time and said suggestions the Barcelona forward - who briefly retired from international football in 2016 - is not committed to the national side are not true.
"Every time Lionel Messi plays he shows that he is a fantastic player, above everybody else, but he needs support from his team-mates," said Sampaoli.
"His human side is amazing. He cries and suffers, he is happy when Argentina win. It's important he shares those feelings. Many people say Leo does not enjoy playing for Argentina, but I don't agree.
"My players play with their heart - they are true rebels."
'Messi turned up for his country'
Messi came to Russia as one of the world's finest players, but had a difficult opening two games - missing a penalty against Iceland and then putting in an anonymous display against Croatia.
But the Barcelona number 10 found his magic on Tuesday with a brilliant opening goal.
"Messi has turned up for his country," former Nigeria international Peter Odemwingie said on BBC Radio 5 live.
"[He has gone] from covering his face ahead of the Croatia game to looking like he meant business before kick-off today. He rolled up his sleeves and contributed for his team."
Former England winger Chris Waddle told BBC Radio 5 live: "Who else? We have talked about him not performing all tournament, but what a finish. Lionel Messi at his very best."
Ex-England defender Rio Ferdinand added that Messi "had a spark and an energy" in the first half and a different "body language" to what we had seen in the first two games.
"Messi is thinking 'this is my stage and my moment," said Match of the Day pundit Ferdinand.
"His goal was what we came to see. The run and two touches before the exquisite finish was what the World Cup needs to be blessed with."
"The greatest players appear in the moments you need them. That's why Messi's the best," said former Argentina international Pablo Zabaleta.
BBC sport
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