Kyle Beckerman and Jamison Olave also scored for Salt Lake (9-3-6).
The loss snapped a streak of three consecutive draws for San Jose (5-7-9).
Both teams were listless on offense for much of the first half. Salt Lake finally stepped up the attack in the waning minutes. Only a good effort from San Jose goalkeeper Jon Busch kept the match scoreless.
Busch came up several huge saves. None were better than his denial of Fabian Espindola in the 43rd minute. Espindola hurdled over an Earthquakes defender and found himself with only Busch to beat for a potential goal. Busch came off the line to challenge Espindola and deftly knocked the ball away as the Salt Lake forward released a shot while racing toward the left post.
Busch came up with another huge save in the 47th minute when he denied Espindola at the end of a long sprint. Espindola tried to force a near angle shot past Busch at the left post, but he calmly parried the ball away to stop the chance.
Salt Lake appeared to break through in the 57th when Nat Borchers ran onto a free kick from Beckerman and headed it right under the crossbar. Borchers was whistled offsides on the play, however, and the goal did not count.
Saborio broke the scoreless draw on a penalty kick in 60th minute, sending the ball past a diving Busch inside the left post.
The penalty kick resulted when San Jose defender Bobby Burling brought down Saborio on a hard tackle inside the box. Burling was shown a red card and ejected moments later, leaving the Earthquakes a man down for the remainder of the match.
Saborio made it 2-0 on an unassisted goal in the 75th. Ned Grabavoy tried to curl the ball past Busch and he poked the ball away. Saborio latched onto it on the rebound and buried it inside the right post.
Beckerman got his second goal of the season in the 79th and Olave closed the scoring in the 83rd with his second.