Having already lost to Canada, the U.S. needed to beat El Salvador in Nashville in their Group A encounter on Monday and were moments away from completing the task.
The U.S. had roared back from a 2-1 deficit to take a 3-2 lead, thanks to German-born forward Terrence Boyd's second strike of the match and a Joe Corona goal just four minutes apart midway through the second half.
The home fans' celebrations were silenced five minutes into injury time, however, when Jaime Alas scored for El Salvador to snatch a last four berth at the expense of their opponents.
Cuba, who drew with Canada earlier on Monday, were also eliminated.
Group B action concludes on Tuesday with Mexico having already claimed one of the berths and Honduras, Trinidad and Tobago and Panama battling for the last spot in the semi-finals to be played in Kansas City.
The two finalists from the CONCACAF region will advance to London regardless of the result.
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