Violence mars Ronaldinho show in Libertadores
Ronaldinho had inspired Atletico, who had already qualified for the knockout phase, with two goals as they extended their perfect record in South America's elite club competition to five wins in five Group Three matches.
Atletico, emerging as favourites to win the trophy for the first time, did fellow Brazilian side Sao Paulo a favour since they are vying with Arsenal for the group's other berth in the round of 16.
Sao Paulo and Arsenal have four points apiece but the Brazilians can pull away if they beat Bolivia's The Strongest at high altitude in La Paz on Thursday.
Brazilian police, who have a reputation of taking to the pitch at the slightest hint of trouble, were quick to use force to control angry Arsenal players who had confronted the match officials at the final whistle, including pointing guns at them.
However, Minas Gerais police lieutenant colonel Cicero defended his men's actions.
"It was criminal conduct, out of place at a football match. [The Argentines] could be arrested," he was quoted as saying on the Globo internet portal.
There was also anger at La Bombonera, where six times South American champions Boca Juniors beat Barcelona 1-0 in Group One, from the Ecuadorean side's Argentine coach Gustavo Costas, who claimed they were denied a blatant penalty in the dying minutes.
Boca, who had gone ahead in the ninth minute with a goal from young striker Nicolas Blandi, were lucky the referee waved play on after central defender Matias Caruzzo missed the ball and brought down striker Damian Diaz inside the box.
"It's a disgrace, everyone saw [the penalty]," Costas told reporters.
"We're leaving with nothing and very angry because the referees are taking us out of the Cup. They are penalties everyone can see and they're forgotten because Boca are still in the Cup."
Boca, who lead the group with nine points, will qualify if Uruguay's Nacional beat Toluca of Mexico in Montevideo on Thursday. Nacional have seven points, Toluca five and Barcelona three.
Holders Corinthians and Mexican debutants Tijuana secured the two qualifying berths in Group Five.
The Brazilians beat Millonarios of Colombia 1-0 in Bogota with a second half goal from Danilo, while Tijuana held San Jose 1-1 in the Bolivian city of Oruro high up on the Andean plateau.
Chilean champions Huachipato, who began the night bottom of Group Eight with four points, climbed back into contention with a 4-0 rout of Caracas FC in the Venezuelan capital.
They now lead the group with seven points, the same number as Fluminense, who face third-placed fellow Brazilian side Gremio, who have six points, away in Porto Alegre next week.