The men were among a group of 22 Uighurs arrested at a camp in the mountains of Afghanistan after the US-led coalition bombing campaign began there in 2001, a month after the September 11 attacks on the United States.
The Uighurs -- members of a mainly Muslim minority who have long accused China of discrimination -- were cleared years ago of wrongdoing and had been staying in a special part of the prison with a library and recreational space.
After this transfer, the first since January 2011, three Uighurs remain at the US-run prison camp in Cuba.
"Negotiations with our allies are continuing to try to repatriate the others," Pentagon spokesman Lieutenant Colonel Todd Breasseale told AFP. He said the pair were in El Salvador after departing Guantanamo on Wednesday.
"These detainees were subject to release from Guantanamo as a result of a court order issued on October 7, 2008 by the US District Court for the District of Columbia, and are voluntarily resettling in El Salvador," the US Defense Department said in a statement.
"The United States coordinated with the government of El Salvador to ensure the transfer took place in accordance with appropriate security and humane treatment measures."
El Salvador`s foreign ministry confirmed that the two Uighurs were on Salvadoran soil after their "refugee status" had been approved.
Washington usually seeks to send cleared inmates to their home country. But it has refused Beijing`s demands to repatriate the Uighurs, saying they would face almost certain persecution.
Uighurs hail from China`s western Xinjiang region, which in 2009 witnessed some of the country`s deadliest ethnic violence in years.
Many Uighurs bristle at what they see as cultural and religious persecution at the hands of Beijing, which has sent in settlers from the country`s Han majority. Beijing argues that it has spurred development in the arid region.
The Center for Constitutional Rights, a human rights advocacy group, applauded El Salvador for accepting the two men, dubbing the resettlement a "profound humanitarian gesture."
"This transfer is particularly important because it is the first time that any man detained at Guantanamo has been resettled in Latin America," the center said in a statement.
The other Uighurs have been resettled in Albania, Bermuda, Palau and Switzerland.
After this latest transfer, 169 detainees remain at Guantanamo Bay. The administration of President Barack Obama is hoping that about 100 of them will be repatriated or resettled in third countries. (*)