FC Dallas' Chris Seitz blocked Tommy Thompson's header in the 88th minute, and San Jose's David Bingham stopped Matt Hedges' left-footed shot in the 90th in a 0-0 tie Saturday night.
Both goalkeepers finished with two saves.
The Earthquakes (5-3-5) had many key players missing from their lineup, including Chris Wondolowski, Simon Dawkins, Anibal Godoy and Alberto Quintero because of Copa America call-ups.
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FC Dallas (8-4-3) stayed one point behind the Colorado Rapids for the overall lead in the MLS standings.
San Jose and FC Dallas played to a 2-2 draw in their first meeting of the season on April 9.