Eddie Johnson and Zach Scott scored to give Seattle a 2-0 lead, but Robbie Keane was awarded and converted a penalty kick in the 68th minute on Sunday night that clinched the Los Angeles Galaxy's 4-2 aggregate victory over the Sounders in the Western Conference finals and a spot in the MLS Cup final for the second straight year.
Seattle staged a rally trying to come back from a 3-0 deficit after getting overwhelmed in the first leg of the Western Conference finals last week.
And they were on the verge after Johnson's early goal and Scott's header in the 58th minute pulled Seattle within one on aggregate.
But referee Mark Geiger, who had been the subject of complaints all night from both sides, called Seattle defender Adam Johansson for a handball in the penalty box and Keane converted his fifth goal of the playoffs.
Los Angeles will host the final on Dec. 1 against Houston, a rematch of last year's final won by the Galaxy.
For the second straight year, Seattle's season ended because it was unable to make up a three-goal deficit in the second leg at home.
Seattle's frustration boiled over after the final whistle when Johnson and Osvaldo Alonso both confronted Geiger at midfield while the Galaxy celebrated.
Seattle came out with aggressiveness absent in the first leg when it seemed content to try and pull out a tie and ended up in a 3-0 hole.
In the first nine minutes, Seattle had two corner kicks and a dangerous free kick from just outside the box. Johnson got free for a shot from the top of the penalty area but it went flying over the crossbar.
In the 11th minute, Johnson appeared to get Seattle the lead off a quick pass by Christian Tiffert, but was disallowed as Johnson was offside.
Television replays showed Johnson was onside when the pass was played and the goal should have counted, but it became a moot point moments later.
Scott won a free ball in midfield and sent it ahead to Johnson, who got position on Omar Gonzalez and scored with a left-footed blast giving Seattle a 1-0 lead in the 12th minute.
Seattle continued to press for chances, but was unable to draw any closer by halftime. Los Angeles nearly got a decisive break just before halftime when Mike Magee's shot was blocked in the penalty box and appeared to hit the arm of Seattle's Jhon Kennedy Hurtado, but Geiger immediate waived off any handball call.
Scott scored on a diving header just at the beginning of a corner kick that Tiffert smartly played toward the near post.
It was just the eighth goal for Seattle in MLS play off set pieces all season and gave Seattle more than 30 minutes to try and equalize.
But the handball ended all those hopes and re-established a two-goal cushion and silenced a crowd of 44,575, the largest for a non-final in MLS playoff history and the sixth largest for any MLS playoff game. Keane had two goals and an assist in the first leg.
Josh Saunders played well in goal for Los Angeles, including a key save of David Estrada's point-blank shot in the 90th minute.
Los Angeles was without midfielder Landon Donovan, bothered by tightness in his hamstring.
He'll get nearly two more weeks of rest before Los Angeles goes after a second straight title. It will be their third appearance in the final in the past four seasons.
Dynamo doubles up United on aggregate
The Houston Dynamo advanced to their second straight MLS Cup final and fourth in seven years, tying D.C. United 1-1 Sunday for a 4-2 aggregate win in the Eastern Conference final.
Boniek Garcia scored in the 33rd minute for the Dynamo, which will play on the road in the final.
"It's a path we have to take, so if we have to be road warriors the whole time, then that's what's in front of us," Houston goalie Tally Hall said. "We have a job to do, it doesn't matter if it's a friendly or hostile environment."
Branko Boskovic scored in the 83rd minute for D.C., which has not won the MLS Cup since 2004.
Houston, which won consecutive MLS Cup titles in 2006 and 2007, qualified for the 2013-14 CONCACAF Champions League. But the Dynamo may miss Ricardo Clark for the MLS final — the midfielder reinjured a groin and left in the 66th minute.
After putting 10 men behind the ball for most of the first half, Houston went ahead after Brad Davis picked up a long ball, evaded Marcelo Saragosa and Dejan Jakovic in a run to the endline and with his left foot cut the ball back to Garcia, who from the top of the 6-yard box put the ball into the roof of the net.
"I just wanted to get the ball back across to give him a chance and Boniek finished it," Davis said.
Down three goals in the aggregate, United coach Ben Olsen inserted Lewis Neal for Saragosa at the start of the second half, sent in Hamdi Salihi for Lionard Pajoy in the 57th and five minutes later put in Dwayne De Rosario for Emiliano Dudar.
De Rosario, the 2011 MLS MVP, had missed 10 games since injuring a knee while playing for Canada in a World Cup qualifier on Sept. 11.
United, in the playoffs for the first time since 2007, failed to score more than one goal in any of its last five games. D.C. was missing suspended right back Andy Najar and injured attacker Chris Pontius. "Winning MLS Cup is an uphill battle for any team, so coming in as a wild card is perhaps a steeper climb than most teams have that reach the cup final, but the bigger the hill, the harder we climb," said Hall.