The victory ran San Jose's home unbeaten string to 13 games as the Earthquakes press for a Western Conference playoff berth.
Salinas sent the ball past Union goalkeeper Zac MacMath from a tight angle in the 15th minute after receiving a pass from Sam Cronin.
Philadelphia nearly tied it up in the 49th minute but Keon Daniel's shot struck the post and bounced harmlessly away.
San Jose's Jon Busch later made a save on a header by Aaron Wheeler from 12 yards out and the goalie got another break 6 minutes from time when Sheanon Williams' header from the 6-yard box struck the far post.
Busch made another save in stoppage time on a close-range shot by Michael Farfan.
The Union are now winless in four straight.