San Jose found itself down 2-0 in the 68th minute with Alan Gordon started the comeback, getting his first goal of the season.
The Earthquakes then went down a man after defender Victor Bernardez was issued his second yellow card, but that didn't stop them from tying it up in the 92nd minute when Salinas blasted in a rebound.
Only seconds later, Gordon tallied on a header, giving San Jose (5-7-6) a stunning decision over its Western Conference rivals.
Marcelo Sarvas and Hector Jimenez each scored for the Galaxy (7-7-3).
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