MLS leading all-time leading goal scorer Chris Wondolowski put San Jose up for good just before halftime, while Jackson Yueill added a key second-half goal to help the Earthquakes pick up three road points.
San Jose (10-13-10, 40 points) rallied from an early one-goal deficit then had to hang on to secure the win.
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Albert Rusnak scored twice for Real Salt Lake and Maikel Chang added a late goal in a furious rally that was to no avail. RSL (13-13-6, 45 points) would have set up a chance to clinch a playoff spot with the victory.
The road team won all three matches during the season series.
Rusnak put Salt Lake on the board in the ninth minute. He fed the ball to Damir Kreilach at the top of the box and then Kreilach laid it off to Rusnak as he cut into the 6-yard box. Rusnak unleashed a right-footer into the center of the goal for the early 1-0 advantage.
Fierro leveled the score in the 37th minute after turning a low cross into the box into a perfect equalizer. An unmarked Fierro latched onto the ball near the goalmouth and, without breaking stride, tapped in a left-footer into an open net.
San Jose took the lead in the second minute of first-half stoppage time on Wondolowski's goal, the 170th of his career. He climbed the ladder on a corner kick and headed a cross from Fierro inside the back post for a 2-1 lead for the Earthquakes.
Cowell split a pair of RSL defenders and released a right footer just as he crossed into the 6-yard box to give the Earthquakes a 3-1 lead in the 69th minute. Yueill rifled a key insurance goal down the middle of the box in the 79th minute.
Salt Lake pulled one goal back in the 85th minute when Chang threaded the ball inside the near post. RSL added another goal in the third minute of stoppage time when Rusnak threaded a goal inside the near post just outside the 6-yard box.
Cade Cowell lays waste to RSL defense on sensational goal
San Jose takes the ball end to end in 12 seconds as Cade Cowell dances through a pair of RSL defenders before knocking in a goal.