Amnesty International said the ruling was "a victory for the rule of law and human rights", adding that the US should ensure that "those held in Guantanamo should be either released or brought before civilian courts on the US mainland".
The Council of Europe, the European Union's human rights watchdog, also praised the decision.
"This is a victory for justice in the campaign against error, ineptitude and hypocrisy," Terry Davis, the Council of Europe secretary-general, said on Thursday.
Lieutenant Commander Charles Swift, a lawyer for Salim Ahmed Hamdan, a former driver for Osama bin Laden who was the defendant in the case before the court, said the ruling was "a rebuke for the process".
Another lawyer for one of the inmates facing charges before a proposed military tribunal added that it was "a fantastic victory" which proved that George Bush, the US president, was not above the law.
The lawyer appointed to defend Australian Guantanamo detainee David Hicks said he was not surprised by the ruling.
"The military lawyers who have been defending the defendants at Guantanamo have been saying this all along. Any real lawyer who isn't part of the administration knows this violates the Geneva Conventions," Michael Mori said.
The United Nations also welcomed the decision, albeit cautiously.
"On the merits, it would seem to be a vindication of the need for vigilance in the protection of all human rights, including those of persons suspected of terrorism," said Jose Luis Diaz, a spokesman for UN High Commissioner for Human Rights Louise Arbour.
Others praised the decision but remained sceptical about whether the ruling would make much of a difference.
"A lot of us remain sceptical of what this decision will actually accomplish, because it only applies to the handful of men who have been charged and Bush has not respected past court decisions," said British former detainee Moazamm Begg, 37, who was held for more than two years at the prison camp without charge.
"Bush has not respected past court decisions"
former Guantanamo detainee
"That said, I'm very glad to hear the news and hope it will be the beginning of the end for many of these men. I also think it will ease tensions here."
Farhat Paracha, whose husband was sent to Guantanamo in 2004 after 15 months at a detention centre in Afghanistan, said that despite the ruling there was "no justice".
"They have no rights, even don't have status of prisoners of war," she said.
"It reminds me the medieval era... Really, it is not serving any purpose but triggering more and more hatred."