Osvaldo Alonso and Lamar Neagle both struck in the second half for the Sounders but they could not overcome the three-goal lead RSL had from the first leg of the Conference semi-final on the weekend to lose 3-2 on aggregate.
Real Salt Lake now move through to the Conference finals, where they will take on the winner of the LA Galaxy v NY Red Bulls, but head coach Jason Kreis said qualification did not come without its worries.
"It's gonna be [a different game] if they get that early goal there," Kreis said. "They put us under a lot of pressure in that first half."
Goalkeeper Nick Rimando was also worried at times but complimented his teammates for sticking at their task.
"We battled," said Rimando. "It was one of those games we had to battle and stick in there to the end. We stuck in there, and we advance. It's a loss, but it feels like a win for sure."