A Juan Rodriguez penalty after 28 minutes opened the scoring while Herculez Gomez made it 2-0 after 75 minutes.
Queretaro were reduced to 10 men when Adrian Arias received a second yellow card after 29 minutes while Israel Martinez walked for the same offence after 48 minutes.
Monterrey are third, four points behind the leaders, after a 4-0 win over Estudiantes Tecos.
Humberto Suazo opened the scoring after a minute, while further strikes by Cesar Delgado (14), Angel Reyna (65pen) and Aldo De Nigris (68) made sure of the points.
Tijuana are up to sixth place after a 2-0 win over Atlas.
Jose Sand (19) and Raul Enriquez (69) scored the goals for Tijuana but lost Joshua Abrego to a 66th-minute red card. Atlas also finished with 10 men after losing Leandro Cufre to a 57th-minute dismissal.
Guadalajara beat Toluca 2-0 thanks to goals by Omar Arellano (24) and Hector Reynoso (62pen). Edgar Duenas was dismissed for Toluca two minutes from full-time.
Atlante were 3-2 winners at San Luis. The visitors took the lead through Osvaldo Martinez after 27 minutes, while the same player added his second after 51 minutes to cancel out Jesus Chavez's 32nd-minute equaliser.
Substitute Michael Arroyo made it 3-1 in the 81st minute but Atlante were then reduced to 10 men when Oscar Vera was sent off in the 84th minute.
Cesar Villaluz Martinez grabbed a second for San Luis after 86 minutes but Atlante held on.