The Chivas were caught at the top of the overall standings with 31 points by title holders Monterrey but remain runaway leaders of Group One, eight points ahead of Toluca and 11 clear of Atlas with three games to go.
The top two in each of the three groups and the two next best placed teams overall qualify.
America beat Chiapas 3-1 away with two goals from Argentine playmaker Daniel Montenegro to remain in the hunt for a place in the last eight from Group Two.
Montenegro opened the scoring at the Victor Manuel Reyna stadium in the southern state of Chiapas in the seventh minute, before he grabbed his second seven minutes later.
The home side pulled one back after half an hour when midfielder Guillermo Cerda scored an own goal under pressure from Colombia striker Jackson Martinez.
However, Chiapas were reduced to 10 men in the 73rd minute when Oscar Razo was sent off for a foul on Brazilian Rosinei and three minutes later, America made sure of the points with a goal from Antonio Lopez.
Toluca won 1-0 away to Queretaro behind closed doors due to a suspension on the home side's La Corregidora ground after fan violence in their previous match left several people injured.
Monterrey, held 1-1 at home by lowly San Luis, lead Group Two by seven points from Morelia and 10 ahead of America.
Santos Laguna, away to Pumas UNAM in Mexico City on Sunday, lead Group Three by one point from Cruz Azul and three ahead of Pumas.
Cruz Azul had a weekend trip to forget to the Caribbean coast to face Atlante in Cancun.
Before being beaten 1-0, players had belongings stolen from their bags during the flight.
"After a quiet flight, on checking their possessions, they all realised that their padlocks had been broken and their bags opened where they had personal items," the club said in a statement.
