The club issued a statement condemning the behaviour of the supporters at Sunday's league match after a protest from the Bolivian embassy in Buenos Aires.
"Independiente wants to express its utmost repudiation at the attitude of a small group of misfits who, after evading the controls at the entrance to the stadium, brought in flags which provoked discriminatory acts against the citizens of our brother countries Bolivia and Paraguay," said the club.
"Our club has a long tradition of peace and non-discrimination," added the club on its website statement.
Boca Juniors have traditionally enjoyed widespread support among the working class and their fan base is reputed to include substantial numbers of immigrants from Bolivia and Paraguay.
Rival fans often use the terms Bolivian and Paraguayan as an insult.
The Bolivian embassy said it wanted concrete action and called on the Argentine Football Association (AFA) to respect its own rules.
"Argentine media published photos in which supporters of Independiente used Bolivian flags to insult their Boca Juniors rivals.
"The Bolivian ambassador believes that in the face of the numerous cases of xenophobia and discrimination in football against the Bolivian community resident in Argentina, verbal apologies are no longer sufficient and concrete and effective action is required," it said in a statement.
"The Argentine Football Association has approved rules which sanction supporters, players, directors, referees and all citizens who are involved in these repugnant acts."
Argentina visit Bolivia for a World Cup qualifier on April 1.
