One of the men was transferred to Estonia, while four others were transported to Oman, which borders both Saudi Arabia and Yemen.
With the five prisoners removed from the facility, the prison now houses 122 prisoners including 54 who have already received approvals for transfer. Of the 54, authorities said 47 of them were Yemenis.
The prisoners who were in this most recent release all had been clear to be transferred for close to five years, but could not be returned to Yemen due to concerns they would eventually join up with existing terrorist fighters.
The conditions for the release of the 5 were not released by Pentagon officials.
Recent conditions over security in Yemen made it more difficult for the White House to transfer any prisoners there, even though President Obama lifted the ban that had been self-imposed in 2013 of transferring Yemenis to Yemen.
The White House has transferred most Yemenis to a number of other countries including recent ones to Slovakia, Georgia and Kazakhstan.
This however, was the first time that Estonia and Oman accepted the detainees from the Guantanamo Bay facility. Oman is a strong ally of the U.S. that played host to many meetings over the nuclear talks with Iran.
John Kerry the Secretary of State in the U.S. met with Sultan Qaboos bin Said al Said the ailing Oman leader on Saturday in Munich.
Pentagon officials said that Akhmed Abdul Qadir one of the detainees was moved to Estonia, while the other four went to Oman.
This past Tuesday, a group of U.S. senators from the Republican Party proposed new legislation seeking to cut the ability of President Obama to transfer suspects in terrorism out of the Guantanamo Bay facility.
The legislation includes barring any transfers to the country of Yemen and to other countries where prisoners who have been released are found later, to have returned to take part in terrorist related activities.