Leon were two goals up by half-time thanks to strikes from Einsner Loboa (15) and Matias Britos (33).
They extended their lead when Nelson Maz netted from the spot on the hour before Hector Mancilla finally put Atlas on the board 14 minutes from the end.
The win put Leon two clear of Toluca and Tijuana and three clear of Club America, all of whom have one game left to play before the play-offs.
Morelia booked their place in the play-offs by beating Santos Laguna 2-0 thanks to a goal in each half from Miguel Sabah.
It left Santos in the eighth and final play-off spot with three teams in a position to catch them over the weekend.