Abd al-Rahim al-Nashiri has said he was tortured into confessing
The judge overseeing Guantanamo Bay hearings, Susan Crawford, has dropped the charges in the last trial there, the Pentagon says.
President Barack Obama had ordered a delay to conduct a review of all cases.
But the request was refused by Judge James Pohl, who was trying Abd al-Rahim al-Nashiri, a suspect in the bombing of the USS Cole in 2000.
Analysts said the row could have damaged Mr Obama's plan to close the detention centre.
Pentagon officials said Judge Crawford had dismissed the charges against Mr Nashiri without prejudice - meaning that new charges can still be made against him at a later date.
He is expected to remain in custody for the time being.
Pentagon spokesman Geoff Morrell said: "It was [Judge Crawford's] decision, but it reflects the fact that the president has issued an executive order which mandates that the military commissions be halted, pending the outcome of several reviews of our operations down at Guantanamo."
The BBC's Jonathan Beale in Washington says the Obama administration ordered a halt to the trials to give it time to review the cases against all the detainees, and to consider who should be tried and how.
Last week, Judge Pohl said the request to halt Mr Nashiri's trial was "unpersuasive" and ruled that the hearing would go ahead.
His ruling appeared to contradict one of the Obama administration's first actions - to instruct prosecutors to ask for the trials of 21 detainees who had been charged to be delayed by 120 days.
All of the proceedings were stopped, with the exception of Mr Nashiri's trial. He was due to appear at the tribunal next Monday.
Mr Obama is expected to meet members of the families of those killed in the USS Cole attack later on Friday at the White House.
The captain of the USS Cole at the time of the attack, Commander Kirk Lippold, said he was disappointed at the decision to drop the charges.
"Justice delayed is justice denied," he told the BBC, pointing out that families of those killed had already waited eight years for a trial.
'Values and ideals'
The attack on the USS Cole while it was moored off Yemen left 17 US service personnel dead and 50 injured.
Mr Nashiri was arrested in the United Arab Emirates in 2002 and eventually transferred to Guantanamo.
He is accused of conspiring to help two Islamic militants who steered an explosives-laden barge alongside the ship.
Mr Obama ordered the review of military trials for terrorism suspects last week. He also ordered the closure, within one year, of the Guantanamo detention centre.
He said the US would continue to fight terrorism but would maintain its "values and ideals" as well.
Some 250 inmates accused of having links to terrorism remain in the facility.
The legal process for these prisoners has been widely criticised on the grounds the US military acts as jailer, judge and jury.