The violence followed confrontations between the players as they made their way from the pitch at half-time.
But FIFA assured people on there security plans.
"FIFA has full confidence in the security arrangements developed," the Daily Star quoted FIFA, as saying in a statement.
Players from Argentinian side Tigre claimed they were threatened with guns by security officials in Sao Paulo, the paper said.
"The fight lasted 15 minutes. A lot of security people came to us and attacked us. Suddenly, I realised I had a gun against my chest," Keeper Damian Albil said.
They refused to return for the second half at the Morumbi stadium, claiming their players had been attacked in the dressing rooms during the interval, the paper added. (ANI )