In a statement, the White House praised the work of administration agencies, particularly Immigrations and Customs Enforcement, in deporting Palij.
The deportation came after weeks of diplomatic negotiations.
The US has "initiated successful denaturalisation proceedings" against 16 former Trawniki guards, according to the museum.
Palij, 95, was born in a part of Poland that is situated in present-day Ukraine, immigrated to the United States in 1949 and became a US citizen in 1957. Palij's USA citizenship was revoked in August 2003 by a federal judge in the Eastern District of NY based on his wartime activities and postwar immigration fraud.
"Despite a court ordering his deportation in 2004, past administrations were unsuccessful in removing Palij", the White House said Tuesday. Of the rest, 28 died while their cases were pending and 9 were ordered deported but died in the USA because no other country was willing to take them.
He is the 68th Nazi to be removed from the United States, and was the Justice Department's final active case.
The U.S. Ambassador to Germany, Richard Grenell, said the deportation was the result of a concerted effort by U.S. President Donald Trump.
Foreign Minister Heiko Maas said that "there is no line under historical responsibility", adding in comment to German daily Bild that doing justice to the memory of Nazi atrocities "means standing by our moral obligation to the victims and the subsequent generations".
La nafta volvió a aumentar: es la segunda suba en dos semanas
Bajo ese argumento, la principal compañía del mercado volvió a subir sus precios en los surtidores. Según registros de este diario, el aumento entre el 8 de julio y la última suba promedió un 9,3%.
"During a single nightmarish day in November 1943, all of the more than 6,000 prisoners of the Nazi camp that Jakiw Palij had guarded were systematically butchered", Eli Rosenbaum, then director of the Justice Department's Office of Special Investigations, said at the time.
At least 23 alleged Nazi criminals who are believed to have worked in death camps were already facing charges in Germany and Austria by June, marking a dramatic increase compared with previous decades, according to a document German prosecutors shared with The Washington Post.
"He's going to die soon and we wanted to make sure he didn't die in peace and comfort at home", Grenell told DW.
He said the new German government, formed in March, brought "new energy" to the case.
Washington had tried to expel him for almost two decades after he admitted to federal officials in 2001 that he had been trained as a Nazi guard in 1943.
"The decision to allow Palij to return to Germany was because of the political will and strong commitment of several members of the Chancellor (Angela Merkel)'s team", the embassy said in a statement. Palij said he never served in the military. "We therefore have to wait (to see) whether there will be a new evaluation or whether new evidence appears to underpin the suspicion".
He pointed out that the "hurdle for evidence for accessory to murder" under the German criminal code was much higher than for stripping someone of citizenship. The excuse bought him another ten years, before he finally owned up to his past and his citizenship was revoked in 2003 for his "participation in acts against Jewish civilians".
The Justice Department said Palij served at the Trawniki concentration camp in Nazi-occupied Poland in 1943, the same year that roughly 6,000 Jews were shot to death there in one of the largest massacres of the Holocaust.
He also argued that he had been forced into becoming a camp guard.