The penalty, awarded for a handball by Argentina defender Leandro Desabato, turned chants from local fans against Brazil coach Mano Menezes into joyful celebration at the late victory.
Fans called for the return of Brazil's 2002 World Cup-winning coach Luis Felipe Scolari, unhappy with the trouble Menezes' team with several first choice players were having in creating chances against a second-string Argentina.
Menezes told reporters he had no complaints with the fans and said they had only expressed their disapproval after he brought off Sao Paulo's Lucas, who had been playing well, for tactical reasons.
"The fans have their preferences but my job is to try to make the national team improve and it did and that's how we got a victory in the end," he said.
Neymar said: "I don't think you should jeer during the game, you've got to wait till it's over. No one likes to be jeered, no one likes to be criticised, that's why we give our best [possible] on the field."
Striker Juan Manuel Martinez, who plays in Brazil for Corinthians, passed out wide to Clemente Rodriguez before racing into the box to collect the left back's cross and beating goalkeeper Jefferson with a shot inside the near post.
"It was a lovely move," Martinez told a television reporter on the pitch about Argentina's goal.
"Desabato was fouled in the penalty incident. Anyway, we played well, with an intelligent game plan against a great team. [Brazil] didn't create clear chances."
It was Brazil's second win in four meetings with Alejandro Sabella's Argentina.
The pressure has grown on Menezes since his Olympic team failed to win Brazil's first football gold medal when they were upset by Mexico in the London Games final in August.
"Big Phil" Scolari is out of work having quit Palmeiras last week with the team in the Brazilian championship relegation zone.
