University side Tigres have 16 points from six matches in the Clausura standings, one point ahead of America and three in front of Tijuana and Atlas who beat Atlante 2-1 on Saturday.
Toluca, who visit Boca Juniors in Buenos Aires in their opening match of the South American Libertadores Cup group phase on Wednesday, are 15th with five points.
Tigres, who won the Apertura title in 2011, scored through Brazilian Juninho, Argentines Lucas Lobos and Emanuel Villa, the first division's top scorer with six goals, and Luis Garcia.
Edgar Duenas pulled a goal back for Toluca.
America, down to nine men from the 38th minute, went in front with a penalty from Paraguayan midfielder Osvaldo Martinez in the 12th minute at Tijuana's Caliente stadium.
The Eagles then had Argentine midfielder Rubens Sambueza sent off in the 21st minute for a second booking and Colombian defender Aquivaldo Mosquera was shown a red card in the 38th for a tackle from behind on goal-bound Fernando Arce.
"(The dismissals) happened to us because we were silly, we need to be more aware," America coach Miguel Herrera told reporters.
"The team showed the same determination we have all tournament, we played against a major team who are the champions and we were almost perfect."
America put up strong resistance in the second half and increased their lead from a 54th-minute counter attack when Paul Aguilar scored with a powerful long-range shot.
Tijuana pulled one back in the 76th minute when Paraguay defender Pablo Aguilar converted Raul Enriquez's cross.
"The defeat hurts. We couldn't manage to score and were well beaten. We had to lose one day," said Tijuana's Argentine coach Antonio Mohamed.
Guadalajara won for the first time in the championship, beating Monterrey 1-0 away on Saturday with Mexico striker Rafael Marquez Lugo's 100th first division goal.
The Chivas are in mid-table with seven points from six matches.
Queretaro's new coach Ignacio Ambriz, who took over in midweek from the sacked Sergio Bueno, marked his first match in charge with a 1-1 draw at home to bottom team Chiapas on Saturday.