Carlos Pena and Mauro Boselli struck at the Estadio Leon, putting Gustavo Matosas' men in prime position for their first title since 1991-92.
Miguel Herrera's America return to the Estadio Azteca on Sunday needing a good win to claim their 12th championship and go outright top as Mexico's most successful club.
Pena only needed 11 minutes to open the scoring in the two-legged final, capitalising on a poor clearance.
A cross from the right was partially cleared into a dangerous area by Aquivaldo Mosquera, with Pena taking a touch before volleying past Moises Munoz.
Matias Britos thought he had won a penalty for Leon just moments later when his pass struck Juan Carlos Valenzuela's arm inside the area, but the appeals were turned down.
America had a header cleared off the line in the first half while Britos was denied by Munoz after the interval.
The visitors had their chances, but it was Leon who doubled their advantage in the 77th minute.
Boselli was freed down the left side of the penalty area before finishing with a delightful chip over Munoz from a difficult angle.
It was Boselli's 15th goal in the Liga MX this season and eighth in the past six games, giving Leon a huge advantage.
Get the best features, fun and footballing frolics straight to your inbox every week.
Thank you for signing up to Four Four Two. You will receive a verification email shortly.
There was a problem. Please refresh the page and try again.