"We want to express our total and utter repudiation at this discriminatory act against Paraguayans and Bolivians by a group of misfits," said Congressman Victor Rios as members voted in favour of a motion to condemn the incident.
Paraguayan and Bolivian flags with the number 12 marked on them were waved by Independiente supporters during the first division game in Buenos Aires on Sunday.
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.
Their supporters are often known as "the 12th man" or simply "12". Rival fans use the terms Bolivian and Paraguayan as an insult.
The president of the Paraguayan Football Association (APF), Juan Angel Napout, said he considered the matter closed.
"I don't think that these few represent the majority," he told reporters.
"I think that the great club of Independiente, having had Arsenio Erico as one of its greatest players as well as many other Paraguayans, does not think this way."
One of Independiente's most famous players is Paraguayan striker Erico, who scored an Argentine record of 293 goals for the club between 1934 and 1947.
Independiente have publicly condemned the supporters' behaviour.
