Efforts from long range were missed by both sides in the opening stages, before Chris Wondolowski came close in the 17th with a low strike from inside the box, forcing Chicago goalkeeper Sean Johnson into a good save.
Chances proved to be a rarity for long periods of the first half, but Harrison Shipp came close to breaking the deadlock for Chicago in spectacular fashion in the 40th minute when his curled effort sailed just over the crossbar.
It was San Jose who scored the crucial opener just before the break as the hosts countered quickly to set up Shea Salinas, who fired past a helpless Johnson.
Another fast break from the Earthquakes produced a second goal in the 52nd minute as Atiba Harris tapped the ball into an empty net after Wondolowski saw his shot saved.
Clever work from Yannick Djalo with little space on offer allowed the hosts to extend their lead further 10 minutes later as an inch-perfect pass found Wondolowski, who finally got his name on the scoresheet with a calm finish.
However, the gloss was soon restored to the scoreline by the hosts when Djalo drilled home San Jose's fourth, before Cordell Cato finished off a flowing move with a fifth of the evening in the 84th minute.