Chris Wondolowski became a 10-goal scorer for the 10th straight season, but Sporting Kansas City rallied to for a 2-1 victory in Kansas City, Kansas, to send the Quakes to their second straight loss.
San Jose (11-9-5) is winless in its past three games following a four-game winning streak.
Sporting KC (8-11-7) snapped a two-game skid and won for just the second time in their last six games.
Leading the comeback was Graham Smith, who scored his first MLS goal in the 76th minute. Benny Feilhaber connected in the 50th minute for Sporting Kansas City.
Smith tapped in a rebound from point-blank range to make it 2-1.