Brazil were on top early on but Argentina took the lead after 19 minutes when a good team move involving 12 passes was finished off by Juan Manuel Martinez's volley.
The Corinthians forward's goal put Argentina ahead but six minutes later Paulinho headed in following a precise free-kick from Neymar.
Argentina tried to defend for large periods and Brazil were unable to put much pressure on goalkeeper Oscar Ustari.
Neymar was kept in check by Velez Sarsfield's young defender Gino Peruzzi and it was left to Lucas to try to find a way through.
Menezes sent on Fluminense duo Thiago Neves and Wellington Nem and Internacional's Leandro Damiao, who replaced Luis Fabiano.
Alejandro Sabella had to take off Arsenal defender Lisandro Lopez because of pain in his left leg, to be replaced by Santiago Vergini.
With the home fans getting restless a hand ball by Argentina defender Leandro Desabato allowed Neymar the chance to score the winner.
"I think the result is not just, we had everything under control but that last move gave no retribution," said Argentina striker Hernan Barcos.
The second leg will be on October 3 at the Bicentenario stadium in Resistencia City, Argentina with Brazil leading in their defence of the Dr Nicolas Leoz trophy.