Nelson Maz netted after two minutes and doubled the visitors' lead on the half hour mark.
Although Atlante pulled a goal back eight minutes into the second half through Cristian Maidana, Leon restored their two-goal lead within a couple of minutes through Carlos Pena.
The Cancun side replied again through Esteban Paredes in the 90th minute - but they could not find an equaliser.
The result leaves Leon just a point off pole position with just one round of matches to play.
Toluca are alongside Leon and Club America on 30 points - but they missed the chance to take over at the top with a goalless home draw with Morelia.
At the other end of the table, Puebla twice came from behind to earn a draw away to fellow strugglers Atlas.
Gregorio Torres and Arturo Gonzalez netted twice for the hosts in the first half, with Matias Alustiza replying.
However, the 83rd-minute dismissal of substitute Sergio Santana gave Puebla a man advantage for the closing stages and they capitalised, with Aldo Polo netting in the 90th minute.