The game was goalless at half-time, but Villa netted five minutes after the restart then again in the 68th and 86th minutes to seal an emphatic win.
Apertura semi-finalists Club America also opened with a win, Rubens Sambueza sealing a 2-1 comeback victory over Monterrey with a 90th-minute penalty.
Monterrey opened the scoring through Walter Ayovi's spot-kick in the 15th minute, but Jesus Molina levelled six minutes before the break and Sambueza intervened in the dying seconds.
Leon were held to a 2-2 draw as substitute Amaury Escoto snatched a late point for Queretaro.
Edwin Hernandez put the hosts, knocked out of the Apertura play-offs by eventual winners Tijuana in the last four, ahead after 24 minutes but Edson Vasquez levelled 12 minutes later.
Matias Britos re-established the lead five minutes after the break, but Escoto ensured the points were shared a minute before the end.
Second-half goals from Abraham Carreno and Hector Herrera gave Pachuca a 2-0 win over Atlante, while San Luis and Santos Laguna drew 1-1.
Herculez Gomez scored for visitors Santos in the 26th minute, but substitute Guillermo Rojas (66) levelled for the hosts, who had Javier Munoz sent off in the 79th minute.