It's TFC's first-ever appearance in a Champions League final.
Chivas took the first leg 1-0 on a goal by Isaac Brizuela on Wednesday in Guadalajara, Mexico.
The Red Bulls racked up 20 shots on the night to just one for the Liga MX side, but couldn't make their efforts count, with Chivas narrowly edging the result.
Toronto hosted the first leg in wins over Tigres in the quarterfinals and America in the semifinals. An away goal in either match further complicates things for the home side.
Toronto goalkeeper Alex Bono made an impressive save in the 27th minute, getting a single hand on a sharp standing header from Club America midfielder Alex Ibarra, deflecting the ball wide of the net.
Bono came up big again five minutes later, throwing his hands up for a close-quarters save on Bruno Valdez, catching his own rebound to quiet Club America's offence.
The Toronto FC goalkeeper stepped up again in the 63rd minute, jumping to get a glove on the ball and tip a well-placed strike from Alejandro Diaz over the crossbar.
As the game wore on Toronto captain Michael Bradley moved further and further back, helping to shore up TFC's defense.
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. They went closest after 18 minutes, when Daniel Royer's teasing low ball from the right across the six yard box eluded his teammates coming in at the far post. His shot was blocked by Toronto F.C.'s wall. Club America scored via stoppage time penalty kick, with Andres Uribe converting the chance.