Brazil, who had beaten Argentina 2-1 in Goiania in September, won the trophy 4-3 in the shootout. The friendly double-header between the teams featured players only from domestic leagues.
The return leg was supposed to have taken place on October 3 but a floodlights failure at the original venue in the northern city of Resistencia forced a postponement until Wednesday.
Scocco, the Argentine first division's top scorer making his international debut at 27, put the home side ahead with a penalty in the 80th minute after Jean brought down Juan Manuel Martinez.
Brazil's Jean made amends four minutes later when he shot across the Argentine goal and Fred wrong-footed goalkeeper Agustin Orion to make it 1-1.
Argentina pushed hard for the winner and in the final minute Walter Montillo launched a quick counter-attack, Martinez fended off two defenders and squared for Scocco to shoot low past Diego Cavalieri.
"We played an intelligent game, we were able to get the win which was what we were looking for, then the penalties are down to luck," Scocco said in a televised interview on the pitch.
"The players had a great game despite having to play a midweek fixture," coach Alejandro Sabella said.
The Argentine coach's squad had been involved in three league matches in the previous 10 days.
Brazil's Neymar had a lively first half, teasing the Argentine defence with his trademark, jinking runs and had a chance in the 33rd minute from inside the box but lifted his lob high over the bar.
Argentina failed to make the most of several free-kicks and corners in the first half with Martinez, who scored a fine opener in the 2-1 win in Goiania, coming close in the 25th minute.
Montillo, occupying the playmaker's role, went on a Lionel Messi-style diagonal run across the face of the goal and fed left-back Leonel Vangioni, whose cross was met by Barcos but his header went just wide.
