Despite the result, Sporting KC remains tied for first place in the Eastern Conference with the New York Red Bulls and two points behind Western Conference leader Real Salt Lake in the Supporters' Shield race.
Sporting KC was limited to only nine shot attempts in Sunday's physical affair. Sporting KC goalkeeper Jimmy Nielsen recorded two saves on the night, both in the first half. His first came in the 33rd minute off a Marvin Chavez set piece.
The Honduran midfielder's curling ball found Clarence Goodson's head 12 yards from goal. Goodson's header appeared destined for the far corner, but Nielsen reacted quickly to palm the ball off the goal line.
San Jose broke through in the 55th minute. Earthquakes midfielder Sam Cronin attempted to play a ball into the Sporting KC penalty box, but Sporting KC midfielder Uri Rosell deflected the attempt.
The ball caromed out wide, where right back Steven Beitashour one-timed the ball to the penalty spot. Wondolowski headed the ball inside the post for his team-leading eighth goal of the season to give the Earthquakes the lead.
Sporting KC nearly answered minutes later. Soony Saad controlled a long ball around an Earthquakes defender and darted toward the endline.
The third-year professional, who turned 21 on Saturday, played a quick pass to a streaking Teal Bunbury but the striker was unable to hit the pass cleanly and the ball sailed over the goal.
Saad was in the middle of the action ten minutes later when Matt Besler hurled a long throw-in into the Earthquakes penalty box. Collin headed the ball to the back post, but Saad appeared to get tangled up with an Earthquakes defender and was unable to connect.
Sporting Kansas City has a quick turnaround as they travel back to Kansas City to prepare for Friday's nationally televised match against the Chicago Fire.
The game kicks off at 7:30 p.m. CT and can be seen live on the NBC Sports Network.