Sao Paulo was awarded the title when Tigre players refused to take the field for the second half of Wednesday's second leg of the final. Sao Paulo was leading 2-0, with the first leg having ended scoreless.
Officials of the Argentine club said their players and staff had been beaten up by security officials in the dressing room area at halftime and guns were drawn. The trouble off the pitch followed scuffles between the two teams at the end of the first half.
Nestor Gorosito, the coach of Tigre, declined to take his team back on the field for the second half. He said unspecified security officials pulled guns on his players while others clubbed players and team officials.
"They pulled two revolvers," he said, referring to unspecified security officials. "We're not going to play anymore."
The chaotic scenes in Sao Paulo, before a sellout crowd of 65,000 at Morumbi stadium, will dismay FIFA — the governing body of world football — which has already been frustrated by slow preparations for the World Cup.
Most of FIFA's angst so far has been focused on getting stadiums and new infrastructure in place. Now security also looms as a concern for the World Cup, which will be played at 12 venues across the country.
Violence on and off the pitch still blights many matches in South America, with Brazil and Argentina particularly troubled. For the World Cup, FIFA relies on local officials and police to enforce safety and stadiums, with Wednesday's event raising doubts about Brazil's capability of doing so.
The Confederations Cup, a preparatory event for the World Cup featuring eight national teams, will be played next year at six venues in Brazil.
The trouble at the Morumbi stemmed from confrontations between the two sets of players following a first half in which the hosts had taken a 2-0 lead, with goals from Lucas and Osvaldo.
It was unclear what happened in the dressing room area, but Argentine television showed what appeared to be blood spattered on walls. Argentine television also showed several Tigre staff members with bruises and bloody faces.
"Police entered and struck our players with clubs," Gorosito told Argentine television. "It was crazy. What happened was crazy."
Romer Osuna, a Bolivian official with CONMEBOL, South America's governing body of football, said Tigre players were afraid to return to the field.
"The Tigre people declined to play because they considered security was not good enough," Osuna told Fox Sports.
Referee Enrique Osses of Chile awarded the victory to Sao Paulo after waiting about 30 minutes for Tigre to retake the field.
Sao Paulo scored twice in five minutes in the first half — a left-footed drive from Lucas in the 23rd and a lobbing shot from the right wing by Osvaldo in the 28th.
Sao Paulo, one of Latin America's most famous clubs, is a three-time winner of the Copa Libertadores; South America's most prestigious club tournament. It has also won the Club World Cup once, and twice won the Intercontinental Cup, the predecessor to the Club World Cup.
This was the club's first Copa Sudamericana title.
The modest Argentine club Tigre was playing in its first international final and has never won the Argentine first-division title.