The opening 45 minutes of the match saw three goals, a red card and a saved penalty kick.
Dallas striker Blas Perez opened the scoring in the 18th minute. A throw-in made its way through the penalty area and was chased down by Fabian Castillo, who turned and crossed for Perez to volley in first-time.
Atiba Harris leveled the score in the 27th minute. Steven Lenhart chested a Shea Salinas corner down to Harris - although Dallas players were alleging a handball - and Harris teed up to drive it in low.
The Hoops were once again on the unpleasant end of the referee's decision when Adam Moffat was shown a second yellow card in the 37th minute and sent off.
San Jose made the advantage count not long before halftime. Jean-Baptiste Pierrazi collected a ball in midfield and had a shot from distance which beat Chris Seitz and found the top corner.
And it was almost 3-1 before the break when Jordan Stewart collided with Castillo on the box in stoppage time, but Jon Busch was up to the job and saved Castillo's shot.
The win is San Jose's second in a row and its third in four games. The Earthquakes move to sixth in the West with their 4-4-4 record. FC Dallas, now an excruciating eight games without a win, is 5-7-3.