The visitors took an eighth-minute lead through star midfielder Dwayne De Rosario who curled a superb shot past Jon Busch for his second of the season but the Quakes quickly replied via Steven Lenhart who hammered home a 19th minute volley.
Two minutes later, Chris Wondolowksi joined Thierry Henry on nine season goals with a simple finish before Justin Morrow's deflected shot encroached DC keeper Joe Willis' goal for the third time.
DC made it 3-2 in the 64th minute when Daniel Woolard finished with a diving header at the backpost from Andy Najar's cross near the byline on the right but soon enough San Jose had restored their two-goal lead when Wondolowski grabbed his 10th of the season in the 69th minute with a powerful header.
Lenhart then added his second five minutes later when he knocked in Marvin Chavez's effort which had rebounded off the crossbar prior to DC netting an 88th minute consolation through Hamdi Salihi who produced a deft finish from De Rosario's pinpoint through ball.
The win allowed San Jose to overtake Eastern Conference leaders Sporting Kansas City on points whilst DC remained second, six points in arrears of SKC, despite the heavy defeat.