Toronto FC entered the second leg trailing 2-1 after losing the first leg at home, and the Canadian club found itself with a massive hill to climb after conceding inside the first 20 minutes.
Orbelín Pineda's opening goal delighted the home fans. With Chivas sitting two goals in front of TFC on aggregate and having dominated the opening run of play, things were looking up for the Liga MX side.
The joy wouldn't last long.
Jozy Altidore's calm finish had Toronto level on the night just six minutes later, slotting home after great work from Nicolas Hasler set the table.
TFC would then turn to Sebastian Giovinco.
The former Juventus playmaker had been booked 43 minutes in after confronting the referee, but moments later he pulling his club level.
Marky Delgado's pass set the Italian free down the left and he made easy work of turning back on his defender before picking out the lower corner to put Toronto in front on the night and level the tie at 3-3 on aggregate.
Chivas piled on the pressure in the second half, striking the woodwork one and forcing several big stops out of Toronto goalkeeper Alex Bono to stay in the match, but Toronto had a chance to win it late.
Giovinco's floated cross found Delgado alone in the box, but the 22-year-old couldn't keep his finish down and the match would finish 2-1 in favor of the MLS side.
With no extra time in the CONCACAF Champions League, the final jumped straight to penalties.
Chivas was perfect from the spot, converting their first four, but Toronto could not match.
Jonathan Osorio was the first to miss, striking the crossbar with TFC's second attempt, and Michael Bradley, Toronto's fourth shooter, sailed his shot over the bar and into the stands to send the home fans into wild celebrations.