The ex-leader is serving 27 years in prison for plotting a coup in 2022.
Four Supreme Court judges ruled in favor of the prosecutors, who charged Eduardo Bolsonaro with "threatening judicial authorities and officials from other branches of government" by saying he would secure US sanctions "if the proceedings did not end" well for his father.
"It is not the role of a Brazilian federal deputy to lobby abroad against their own country," said Judge Alexandre de Moraes.
The 41-year-old will also be barred from holding public office for eight years, a decision he may appeal.
"The real purpose of this senseless trial is only one: to remove my name from the elections," read a statement from Bolsonaro, who was planning to run as a substitute Senate candidate in elections in October.
More from WorldAt first, Bolsonaro's ploy worked. Last year, US President Donald Trump hit Brazil with steep tariffs as punishment for what he called a "witch hunt" against Bolsonaro senior.
However, the duties were lifted after a first official meeting between leftist President Luiz Inacio Lula da Silva and Trump.
The Trump administration had also sanctioned Supreme Court Judge Moraes, but those measures were also lifted.
Relations between Brasilia and Washington are going through a rough patch after Trump met with Eduardo's brother and presidential candidate Flavio Bolsonaro ahead of elections, in which polls suggest Flavio Bolsonaro and Lula are running neck and neck.
In December, Eduardo Bolsonaro was stripped of his seat in the lower house of parliament for his excessive absences.
