Lenhart headed home a Shea Salinas corner kick from the top of Seattle’s 6-yard box in the 93rd minute. The Earthquakes (14-5-5) moved four points clear of Sporting Kansas City, their nearest pursuers in the Supporters’ Shield chase.
Simon Dawkins put San Jose ahead in the 71st minute, but Fredy Montero appeared to save a road point for Seattle with a 92nd-minute header from point-blank range on a weak San Jose clearance.
That was before Lenhart struck for another late goal for San Jose, which has scored a league-best 17 times after the 75th minute this season.
San Jose is unbeaten in its last 13 matches at home, going 9-0-4 since Aug. 13, 2011.
The loss snapped a six-game MLS unbeaten streak for the Sounders (10-6-7), who were playing their third match in seven days.
Dawkins wheeled on a headed pass from Lenhart and beat Seattle goalkeeper Michael Gspurning to the near post from 12 yards.
Seattle forward Sammy Ochoa, making his first career MLS regular-season start as the busy Sounders battled fatigue, put a ball off the crossbar in each half, finding the woodwork with a 32nd-minute bicycle kick and a 59th-minute header.
The Sounders had chances to equalize in the closing minutes but couldn’t cash in. Eddie Johnson pushed a header just over the crossbar in the 73rd minute, and Brad Evans’ booming shot from 14 yards was blocked with a full-body slide by San Jose midfielder Sam Cronin.
The win was a measure of revenge for San Jose, which was knocked out of the U.S. Open Cup by Seattle in a contentious June 26 quarterfinal.