Valencia went off with a calf injury in the seventh minute of the game, with Manchester United boss Jose Mourinho’s already depleted full-back options restricted further with his enforced withdrawal.
The extent of Valencia’s injury is not yet known, but Mourinho will hope his first-choice right-back recovers in time for United’s Premier League opener at home to Leicester on August 10.
A crowd of 65,109 watched United draw 1-1 with Real Madrid at the Levi’s Stadium last year, but this time around just 32,549 turned out in the 68,500-capacity arena, even with tickets changing hands for as little as $10.
There was a smattering of boos at the final whistle after the drab encounter, with United never looking like scoring in a game low on chances and entertainment.
United came close to taking the lead inside five minutes, Alexis Sanchez floating in a free-kick which was met by Eric Bailly, who thudded a header against the underside of the bar.
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Sanchez, despite having only joined up with the United squad at their Los Angeles training base 48 hours earlier, started the game and looked sharp and dangerous on the ball.
The Chile star, who has enjoyed a full summer off for the first time since 2013, surged forward in the 17th minute, only to be taken out by Florian Jungwirth, who was duly cautioned for the foul.
Jungwirth showed a softer side to his character moments later when he took off his shirt and used it to scoop up a dead bird from the pitch, dispatching the creature to the sidelines.
Timothy Fosu-Mensah, on as a second-half sub, cleared off the line an effort from Earthquakes forward Vako just before the hour, while Lee Grant, who replaced Joel Pereira, produced a fine save to deny Tommy Thompson.