The 1-1 result at Red Bull Arena in the second leg put the Sounders through 4-2 on aggregate, following their comfortable 3-1 win in last week's first leg.
Given what was at stake, it was a fiery opening from the outset, with elbows leading and City's Valentin Castellanos earning a yellow card in onl the opening minute.
The Sounders put themselves in the box seat in the 28th minute, though, with Raul Ruidiaz scoring and getting the Sounders 4-1 ahead on aggregate.
City had the proverbial mountain to climb even after Santiago Rodriguez's goal in the 51st minute, but Stefan Frei still came to the rescue for Brian Schmetzer's side, coming up with important reflex saves on multiple occasions in the second half.
The Sounders will now face Pumas UNAM in the Champions League final, after they saw their way past Cruz Azul on Tuesday.
It marks only the fifth time since 2010 that North American club football's showpiece has not been contested by two Mexican teams.