The charges were laid against Thomas Gibson, a sergeant, Philip Wolford, a captain, and Philip de Camp, a lieutenant colonel, by Judge Santiago Pedraz in April 2007.
The court said the charges should be definitively dismissed, saying there was no further avenue for appeal.
Pedraz had cited the three US soldiers as responsible for the tank shelling on April 8, 2003 of the Hotel Palestine which killed Jose Couso, who worked for Telecinco, a private Spanish private television station.
Another cameraman, Taras Protsyuk, a Ukrainian, died in the shelling while three other staff members of the Reuters news agency were wounded.
Pedraz had argued at the time that the soldiers "knew that the Palestine Hotel (like the zone in which it was situated) was occupied by civilians".
US officials had not responded to the judge's repeated attempts to make the trio face a Spanish court, ignoring two international warrants for the soldiers' arrest issued in October 2005 and January 2007.
A US inquiry carried out in 2004 into the hotel shelling found no fault or negligence on the part of US troops.