The Gallos Blancos won a trophy for the first time as a top-divison team, ending a 66-year hunt for a major title.
It took penalty kicks, but Querataro finally came out on top, beating Chivas 3-2 in a penalty shootout after a scoreless draw to lift the Apertura's Copa MX prize.
The club, established in 1950, had won second-division titles before but a runner-up finish in the 2015 Clausura is the closest it ever had come to a trophy until Wednesday.
Goalkeeper Tiago Volpi made a number of stunning saves in the opening 90 minutes and then not only stopped two penalty kicks during the shootout, including Alan Pulido's attempt that gave Queretaro the crown, but also scored one from the spot to help his own cause.