Brazilian police appeared to spray angry Boca players at the door of their dressing room after the match, with videos showing the players choking as they shouted abuse at law enforcement officers.
Brazilian website Globoesporte said the Boca players tried to get into the home dressing room where the match officials had sought refuge.
The players had clashed in the tunnel after the game in which the Video Assistant Referee (VAR) denied Boca what they believed was a legitimate goal for the second time in the tie.
The last-16 showdown at the Mineirao stadium ended 0-0 and Atletico went through 3-1 on penalties. The first leg in Buenos Aires last week also ended goalless and Boca had a goal disallowed for offside after a long VAR check.
When asked if the refereeing was a factor in their elimination, Boca midfielder Diego Gonzalez said: "Without a doubt, everyone can see that. We scored a good goal, and the fact is that we deserved to win the first game as well.
"This hurts, we feel bad. CONMEBOL [the South American Football Confederation] need to look at the refereeing."
Anger spilled over during the second half when the referee went to check the disallowed goal on the pitch side VAR monitor.
Brazilian officials clashed with Boca players who approached the referee, and assistant coaches from both sides were sent off.
Atletico goalkeeper Everson was the hero, saving two Boca penalties and then scoring the decisive spot kick to put Atletico into the quarterfinals.