The west stand of Chivas's Omnilife stadium was bedecked with banners denouncing players, coaching staff and club owner Jorge Vergara at Sunday's match.
"Leave or you die", "Enough is enough", "You can't mess with history", "Our patience is up", "Mediocre directors" and "Go, Vergara", said some of the banners displayed.
Guadalajara, who with current champions America hold a record 11 league titles but last won the crown in 2006, have been struggling to live up to their big name.
Coach Juan Carlos Ortega brushed off the banners, saying: "I didn't even read or see them, the match was too good to be looking at threats on sheets.
"We already have a very serious worry trying to get the team to win," he told reporters after Chivas's second victory in 16 matches in the championship thanks to a goal from striker Rafael Marquez Lugo.
Guadalajara, three from bottom of the 20-team championship, have failed to reach the eight-team knockout rounds which is a must for Mexico's leading clubs.
America, who qualified with four matches to spare, made sure of finishing top of the table despite a 0-0 draw at Queretaro on Friday and will meet the team finishing eighth in the quarter-finals.
Second-placed Santos Laguna lost 2-1 at Chiapas on Saturday and are four points behind with one round to go in the league phase.
Santos, Cruz Azul, Leon and Toluca have secured places in the last eight with Chiapas, Morelia and Queretaro occupying the other three qualifying berths while UANL Tigres and Tijuana are mathematically still in the running.