Gustavo Matosas' men took a 2-0 lead into the away leg and only built on their advantage against an America side who were unable to get into the tie.
Mauro Boselli netted once more to give Leon the lead before Juan Ignacio Gonzalez's own goal gave America, who finished the encounter with 10 men, hope just before the break.
But second-half goals from Gonzalez - this time at the right end - and Edwin Hernandez sealed Leon's sixth title and first since 1991-92.
Luis Angel Mendoza almost gave America a dream start in the eighth minute.
The attacker used his quick feet to beat two defenders in the area before hitting the inside of the post, seeing his effort bounce clear.
Narciso Mina had failed to make the most of a glorious headed chance for America moments before Boselli's 13th-minute opener.
The lethal Argentine was given a bit of space on the right side of the area and drilled his low shot into the bottom corner.
It was Boselli's 18th goal of the season, adding to his strike in the first leg of the final.
America threatened time and time again, with Mina squandering several headed opportunities.
But they were finally given some hope of a remarkable comeback thanks to Gonzalez's own goal three minutes before half-time.
Rubens Sambueza cut in from the right before curling a left-footed cross which Gonzalez headed past his own goalkeeper William Yarbrough.
But Gonzalez needed just six minutes into the second half to redeem himself for the error.
The defender headed in a corner on 51 minutes, all but giving America no chance of a record 12th Mexican league title.
If Miguel Herrera's men had hope, it was dashed just four minutes after Leon regained the lead as Francisco Rodriguez was sent off.
With Matias Britos through on goal, the defender dragged down the Uruguayan, denying an obvious goalscoring opportunity to be given his marching orders.
Leon were in party mode and made it 3-1 in the second leg thanks to Hernandez.
Luis Montes found space just outside the area and passed down the left for Hernandez, who took a touch before firing into the corner.
Herrera, who leaves America to take charge of Mexico, was sent off late on as Leon cruised to victory.
