The match will take place on April 6 in the Bolivian city of Santa Cruz de la Sierra.
The Brazilian team would pay their own costs and hand their share of the gate money to Kelvin Beltran's family, CBF President Jose Maria Marin said.
"They will go, play and come back on the same day," Marin said. "It's a sacrifice, but they will do it to show sporting solidarity, not just on behalf of the CBF but from the Brazilian people."
Bolivian police arrested 12 fans of Sao Paulo-based Corinthians, the Libertadores Cup holders and club world champions, and charged them with homicide after a firework set off in the away end hit San Jose fan Beltran, killing him instantly, on February 20.
A 17-year-old Brazilian later turned himself in to authorities and took responsibility. All 13 are still in police custody in Oruro.
Since April 6 is not a FIFA international date, Brazil will field a team picked solely from the domestic league without any of the European-based first choice players.
Coach Luiz Felipe Scolari, who said the friendly would be a show of solidarity between two countries united in grief, welcomed the chance to test players on the fringes of his squad.
"It's always important to be able to bring the national team together," he told the CBF website.
"The more so in another friendly before the Confederations Cup in which more players, who up to now have not had the opportunity, will get the chance to be watched."
Brazil will host the June 15-30 tournament, a kind of dress rehearsal for the World Cup finals they will stage next year.