Atlas were trailing 4-1 to local rivals Guadalajara with just under one hour of the second leg played at the Jalisco stadium on Sunday when one supporter ran onto the pitch and remonstrated with the players.
He was quickly detained, however other Atlas supporters also ran onto the field and tried to attack coach Tomas Boy.
Television pictures showed that both teams ran to the dressing rooms, and the match was suspended until security officials brought the situation under control.
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Pictures also showed riot police clashing with Atlas fans in the stands at both half-time and during the interruption in play.
Atlas president Gustavo Guzman announced after the match that the hardcore supporters' group known as "Barra 51" would be banned indefinitely from the stadium.
"It wasn't just one fan, it was a number of them," he told reporters. "They were running towards Tomas Boy and some of the players came to his defence.
"When we took over Atlas one year ago, we supported the supporters groups and, sadly, today I inform you that they are banned from the Jalisco indefinitely."
The Guadalajara city government subsequently announced on its Twitter feed that the Jalisco stadium, which hosted matches at both the 1970 and 1986 World Cups, was closed until further notice.
There was no further scoring after the teams returned and Guadalajara completed a 4-1 aggregate win.
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