Chris Wondolowski and Ramiro Corrales provided the goals that gave San Jose its long-awaited win.
Wondolowski opened the scoring for San Jose in the 10th minute, getting on the end of a Rafael Baca cross and one-timing a shot past Chicago goalkeeper Sean Johnson.
Dan Gargan came within inches of pulling back a quick equalizer for Chicago in the 17th minute, but his right-footed shot struck the post to keep the Fire at bay.
San Jose had a golden opportunity to double the lead when it was awarded a penalty kick in the 52nd minute. Wondolowski stepped up to take the ensuing shot, but was denied by Johnson, preventing Wondolowski from securing a brace.
The Earthquakes eventually found its second goal in the 69th minute, and it was Wondolowski who turned provider.
San Jose's leading scorer slipped a ball into the box for Corrales, who calmly fired a shot past Johnson to secure the win for the 'Quakes.
The win brings San Jose to within two points of Chivas USA. The Earthquakes remain in eighth place in the West with 29 points, one spot behind seventh- place Chivas with 31 points.
With Toronto FC and the New England Revolution picking up wins on Saturday, Chicago falls into a three-way tie for last place in the Eastern Conference. Each team has 27 points, but Chicago has played 27 matches in comparison to New England's 28 and Toronto's 29.