Xavier Baez scored the winner for Guadalajara just past the hour in Wednesday night's 1-0 win away to Pachuca played in a downpour at the Hidalgo stadium.
Midfielder Baez ran onto a loose ball outside the box and shot into the top left corner of Colombian goalkeeper Miguel Calero's net.
"Playing against Pachuca has become a 'clasico' and it's obvious both teams were in perfect form and played a great match but Chivas had the surer aim," Guadalajara owner and president Jorge Vergara told reporters.
The hat-trick by Atlas midfielder Zepeda, who scored his first goal in the opening minute, was part of a 7-1 rout of Indios Juarez, who have not won in 23 matches.
Zepeda scored again in the 14th minute when he tapped in after goalkeeper Humberto Hernandez spilt a hard drive from Argentine Dario Botinelli and in the 56th.
Champions Monterrey, down to 10 men from the 40th minute after midfielder Luis Perez was sent off for a second booking, beat Estudiantes UAG 4-3 away in Guadalajara with two goals from substitute Abraham Carreno.
Cruz Azul, who have struggled since losing the Apertura final to Monterrey in December, ended a run of four games without victory by beating Morelia 1-0.
Substitute Cesar Villaluz came on 12 minutes from the end for Argentine midfielder Christian Gimenez and scored in the 90th.
CONCACAF Champions league title holders Atlante won their first match of the championship 2-0 against Chiapas at their Cancun home on the Caribbean coast, while shooting victim Salvador Cabanas's America lost again, 3-1 away to Toluca.
