Over 30 other staff members were detained whilst gunmen raided the office of the International Rescue Committee (IRC) in Donetsk.
The raid led to the IRC halting its aid work in Ukraine.
IRC President David Miliband said that aid workers "should never be targeted" and that the raid was an "affront to the IRC's principles".
In a statement the former UK foreign secretary said that the two men were healthy and in a safe location, before condemning their captors.
"The actions taken by the security forces of the self-proclaimed Donetsk People's Republic, including the intimidation of our dedicated humanitarian staff, are an affront to those principles. Every day, the world's humanitarian workers show great courage, taking risks help the most vulnerable in crisis situations. They should never be targeted."
The masked gunmen seized 37 IRC workers on 29 April.
Five international members of staff from Canada, Britain, Georgia and Chile were forced to leave rebel-controlled territory, in eastern Ukraine.
However two US workers were held by officials apparently working for the the self-declared People's Republic of Donetsk Ministry of State Security.
On the day of the raid Russia's Interfax news agency cited a DPR security ministry spokesman accusing the IRC of concealing "eavesdropping equipment" in their Donetsk office.
The spokesman claimed that "foreigners regularly travelled to Ukraine, but not in order to accompany [the IRC on] humanitarian missions".
"Foreign employees established contact with officials in DPR ministries and agencies, showing interest in obtaining information about the situation in the republic," he said.
He also accused the agency of "hiring DPR citizens for work without signing agreements with them, evading the payment of taxes into the DPR budget".
Heavily armed rebels have been fighting government forces for a year in Ukraine's Donetsk and Luhansk regions.
The West says Russia has armed the rebels and sent in regular soldiers - an accusation echoed by independent experts.
Moscow insists that any Russians on the rebel side are volunteers.
Source: BBC News