Riot police moved in to restore order after a few punches were thrown and several players were pushed following Brazilian side Internacional's 5-3 aggregate win over Mexico's Guadalajara.
Within seconds of Inter's win, dozens of people ran on to the Beira-Rio pitch in Porto Alegre to celebrate with the players, reserves, members of their families and officials.
The Brazilian players tried to avoid getting into tussles with the Mexicans and police quickly restored order.
Guadalajara said they reacted to a lack of respect for the Mexican national anthem before kickoff.
"They did not respect the anthem from the start and if they show no respect how can they expect us to respect them?" Mexico midfielder Adolfo Bautista told reporters.
Bautista, who annoyed the Inter fans by warming up during the Brazilian anthem, was quoted in Mexican media as saying a Brazilian team assistant had spat at Marco Fabian de la Mora, who scored Guadalajara's opening goal.
Guadalajara lost the first leg 2-1 at home but raised their hopes of an upset by taking the lead in Wednesday's second leg before going down 3-2.
Their coach Jose Luis Real said his team had allowed the disturbance during the national anthem to affect their concentration.
"We've got to get more used to this type of situation so we don't get distracted," Real told reporters. "But that's not a pretext (for the defeat). Inter are great champions."
In Europe, Champions League regulations ban the playing of national anthems before kick-off, doing away with their potential for inflaming nationalist sentiment.
The Libertadores Cup, inaugurated in 1960, has had a chequered past, particularly in its early days with violent play marring many matches.
In 2005, coach Jorge Benitez was sacked by his club Boca Juniors and fined by a Buenos Aires court after spitting at Bautista in a quarter-final defeat by Guadalajara.
Mexican clubs, which belong to the CONCACAF region, have played in the Libertadores Cup as guests since 1998.
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