Seattle scored twice in the final 10 minutes to overcome San Jose in front of a record crowd of 64,140.
CenturyLink Field packed 64,140 fans inside to watch Kasey Keller's final regular season home game, the third highest attendance for a stand-alone MLS match.
"Games like tonight just grip you," Sounders FC coach Sigi Schmid said.
Keller, 41, is retiring after the season. He made seven saves to keep Seattle in the match.
"He's played so many outstanding games for the Sounders that you sort of, as a coach, sometimes you almost go, 'OK, it's expected,'"Schmid said. "But you can't ever become complacent. You can't ever expect it."
However, Wondolowski found a way past Keller in the first half. A long clearance bounced through to Wondo, who tucked his shot into the back of the net for his league-leading 15th goal of the season.
Seattle didn't reply until the final 10 minutes of the game. Mauro Rosales, marking his return from a knee sprain, chipped a ball over the 'Quakes backline to Sammy Ochoa, who clipped a shot off the post and in for his first MLS goal.
"You could see the impact that Mauro [Rosales] has on our game," Schmid said. "When he came onto the field, he just changed our whole dynamic."
A few minutes later, Fredy Montero prodded a shot home. The Colombian has scored or assisted seven games in a row.
Neither team had anything to play for - Seattle is assured second in the West and San Jose cannot qualify for the playoffs - but the comeback proved a touching sendoff for a U.S. soccer legend.
"This was the most nervous I've been for a game since the World Cup because I just didn't want to disappoint," Keller said. "I'm just humbled. I'm humbled for what the club has done for me - given me the opportunity to come home and finish my career back home in something that is just so incredibly special."