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.
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.
"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.
