Villa, who spent three season at Cruz Azul, struck first in the seventh minute of Saturday's match at the Estadio Azul when he tapped the ball home after Brazilian Juninho's free kick came back off the bar.
The former Derby County striker was on hand again in the 26th when Olympic gold medal-winning goalkeeper Jesus Corona could only parry another shot from Damian Alvarez and the ball fell to Villa, who took his tally as leading scorer to eight.
Cruz Azul, whose fourth match without a victory has left them in 10th place with 10 points from eight matches, pulled one back on the hour through Argentine midfielder Christian Gimenez, who used to enjoy a prolific partnership with Villa.
Unbeaten Tigres lead the Clausura championship with 20 points, three more than Atlas, held 0-0 at Queretaro, and four ahead of America, who lost 1-0 at Santos Laguna on Friday.
Title holders Tijuana, winners of the Apertura championship, are fourth with 16 points after ending a run of two defeats with a 2-0 victory over Atlante.
- Sports & Recreation
- Cruz Azul
- Estadio Azul