Playmaker Christian Gimenez opened the scoring after 20 minutes and centre-back Luis Perea doubled their lead 10 minutes later to seal Cruz Azul's third consecutive victory.
Cruz Azul, who emerged from a worrying slump to win the Copa Mexico knockout competition 10 days ago, are sixth in the standings with 23 points from 15 matches.
The top eight teams at the end of the 17-match league stage of the championship qualify for the knockout rounds.
Leaders UANL Tigres, who have 32 points after Saturday's 3-1 win over Pachuca, second-placed Atlas (31), and America and Santos Laguna (both on 29) have secured quarter-finals berths.
Atlas beat Guadalajara 1-0 with a goal from Rodrigo Millar in their derby at the Jalisco stadium on Saturday.
Guadalajara coach Benjamin Galindo complained of the way Atlas coach Tomas Boy celebrated his team's victory.
"It bothered me because he turned towards our bench and that's not ethical since he too will lose one day and he won't like it if someone celebrates in his face," Galindo said.
Guadalajara have been struggling for more than a year with Galindo unable to turn things round after former consultant Johan Cryuff was sacked in December.
Striker Cristian Benitez, the championship's joint top scorer, headed his ninth goal to give America a 1-0 victory in the Mexico City derby against UNAM Pumas at the Azteca.