The MLS champions and manager Greg Vanney will face Chivas Guadalajara home and away between April 17-19 and April 24-26.
It's TFC's first-ever appearance in a Champions League final.
The New York Red Bulls drew 0-0 with CD Guadalajara on Tuesday night, with the Mexican side heading through to the final courtesy of a 1-0 victory in the first leg. Pereira was observed to commit an act of physical aggression against an opponent - grabbing the throat of Red Bulls midfielder Sean Davis - while the ball was not in play.
Bono charged forward to put his body on a cross in the 77th minute, getting to the ball before a hard-charging Club América forward.
Chivas took the first leg 1-0 on a goal by Isaac Brizuela on Wednesday in Guadalajara, Mexico.
But with a shot account of 20-1 in favour of the Red Bulls, the big winner was Chivas goalkeeper Rodolfo Cota.
Chivas gain the advantage of the second leg at home by virtue of having accumulated the most points in their six matches to reach the final.
Club America, winners of two of the previous three editions of the tournament, applied pressure to get back into the tie but were met only by a string of saves by Toronto goalkeeper Alex Bono. Bono stepped up again in the 63rd minute, jumping to get a glove on the ball and tip a well-placed strike from Alejandro Díaz over the crossbar.
America had a free kick right on the edge of the penalty area in the 84th minute, with goalkeeper Agustin Marchesín coming up to take the shot so his teammates to load up the box. His presence made a difference in the 80th minute when he stopped a potential breakaway from Diaz.
Andres Uribe tied it for Club América in the second minute of injury time on a penalty kick.
It was the second straight Mexican club that Toronto had knocked off in the C.C.L., the top club competition for North and Central America and the Caribbean.
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