But the three-judge panel in Washington said it granted the temporary stay on the order to give the appeals court more time to consider the dispute.
The federal court said the stay "should not be construed in any way as a ruling on the merits" of the government's request.
The US military no longer considers the Uighurs to be "enemy combatants".
But they have been kept in detention at Guantanamo as US officials have been unable to find a country willing to take them.
The US justice department earlier told the appeals court that diplomatic negotiations continued in an effort to find an appropriate country to send the detainees.
'A hard day'
A lawyer for the Uighurs said they were dismayed by the ruling.
"It's a very hard day," said Emi MacLean of the Centre for Constitutional Rights, but she said she remained hopeful the group would be released in time.
The United States allowed five Chinese Muslims released from Guantanamo to go to Albania two years ago.
The US government has said it cannot return the Uighurs to China because they would face persecution.
Many Muslim Uighurs have sought greater autonomy from Beijing for their region and some want independence.
Beijing has waged a relentless campaign against what it calls their "violent separatist activities".
The Uighurs had been living in Afghanistan during the US-led bombing campaign that began in October 2001 before they fled into the mountains and were detained by Pakistani authorities, who handed them over to US troops.
The original ruling in favour of the 17 Uighurs, which was the first court-ordered release of Guantanamo detainees since the prison opened in 2002, had angered the Bush administration, with a spokesman for the department of justice saying it presented "serious national security and separation of powers concerns and raises unprecedented legal issues".
There are about 255 detainees remaining at Guantanamo.
Most have been held for years without being charged and many have complained of abuse.