The penalty, awarded for a hand ball 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's team with several first choice players were having in creating chances against a second-string Argentina.
The match was the first of two between teams drawn only from the domestic leagues of two great South American rivals. They meet again in the northern Argentine city of Resistencia on October 3.
Menezes said 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."
Argentina, on the back foot for the opening 20 minutes, went ahead in their first dangerous incursion into the Brazil penalty area.
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.
Brazil equalised six minutes later from a free-kick taken by Neymar on the right with midfielder Paulinho offside according to television replays when he moved forward to head past goalkeeper Oscar Ustari.
"It was a lovely move," Martinez said 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.
Last year in matches between home-based selections, the rivals drew 0-0 in Argentina with Brazil winning the return fixture 2-0.
Argentina won 4-3 in a friendly in New Jersey between the full national sides in June courtesy of a Lionel Messi hat-trick.
The full Brazil team were also beaten by Argentina 1-0 in Qatar in November 2010 shortly after Menezes was appointed to build a team capable of winning the World Cup at home in 2014, something many fans now doubt.
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.