Saborio broke a scoreless tie in the 71st minute by blasting a lead pass from Joao Plata past San Jose goalkeeper Jon Busch from 17 yards out.
RSL (1-0-0) doubled its advantage in the 85th when the Costa Rican put in a left-footed shot off a feed from Kyle Beckerman.
The Earthquakes (0-1-0), meanwhile, saw their 18-game home unbeaten streak snapped with the loss.
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