Lee Nguyen's late strike proved the difference and gave New England its first victory of the 2014 season.
An own goal from Victor Bernardez handed New England the lead in the 35th minute. The center back slid in the box hoping to knock a loose ball away, but only succeeded in pushing it into his own net.
Earthquakes captain Chris Wondolowski brought the game back on level terms in the 69th minute. Cordell Cato's cross was blocked, but it fell to Wondolowski, who finished from short range through traffic.
New England scored the winning goal in the 93rd minute. A quickly taken free kick released Lee Nguyen down the left wing, and the midfielder made a cut inside Clarence Goodson to fire his shot past Jon Busch.
The win is New England's first of the season, and the Revs are now 1-2-1. San Jose is still looking for its first victory, and its record stands at 0-2-1.