Goals from Matias Alustiza and Sergio Ceballos saw Puebla escape a late comeback effort from Queretaro at Estadio Corregidora.
Tiburones Rojos de Veracruz were crowned Clausura 2016 Copa MX champions following their 4-1 victory over Necaxa.
Necaxa booked their spot in the Copa MX final following a back-and-forth encounter against Cruz Azul.
Atletico San Luis reached the semi-finals of the Copa MX following a dramatic penalty shootout.
With teams from both Liga MX and Ascenso MX in the mix, Rigo Cervantez lists five reasons why you should the Copa MX quarterfinals.
Tijuana advanced to the next phase of Copa MX in second place with 14 points in their group.