Atlas crash, Guadalajara win Mexican showdown
Ramirez became the club's third coach in a month on Thursday, replacing Omar Arellano, who left the club the day before after only three matches.
Guadalajara's goal came in the 68th minute when Sergio Ponce headed in from Alberto Medina's cross after he was left unmarked at the far post.
America were missing championship top scorer Salvador Cabanas through injury but created plenty of chances, only to be thwarted by Guadalajara goalkeeper Luis Michel.
Guadalajara, the only Mexican team not to field foreign players, jumped to second in Group Two with 19 points from 14 games. America dropped to fourth with 18 points.
Atlas' nine-match unbeaten run came to an abrupt halt when they lost 4-1 to Santos Laguna.
Ecuador striker Cristian Benitez scored twice for Santos while Ismael Fuentes put through his own goal and Walter Jimenez completed the scoring. Gonzalo Vargas scored Atlas' consolation.
Atlas, under former Mexico coach Ricardo La Volpe, stayed second in Group Three.
Toluca became the first team to reach the quarter-finals when they beat Chiapas 1-0 with a 90th minute header by Edgar Duenas.