In 1943 he went to the Trawniki SS training camp in Nazi-occupied Poland.
A White House statement said Palij served as an armed guard and had played an "indispensable role" in ensuring Jews were killed.
Immigration and Customs Enforcement agents implemented a deportation order against Jakiw Palij dating to 2004, the network said.
President Donald Trump instructed US Ambassador Richard Greneli to make Palij's deportation a "top priority".
"Through extensive negotiations, President Trump and his team secured Palij's deportation to Germany and advanced the United States' collaborative efforts with a key European ally", the statement read, Fox News said.
The US Department of Justice released a photo taken in 1957 of Jakiw Palij, who illegally concealed his Nazi past from US immigration agents. The U.S. Holocaust Memorial Museum writes that SS police unit shot all 6,000 prisoners. He concealed his Nazi service by telling US immigration officials that he had spent the war years working until 1944 on his father's farm in his hometown, which was previously a part of Poland and is now in Ukraine, and then in a German factory.
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Investigators first confronted Palij about his past 25 years ago but authorities have struggled to deport him.
In August 2003, a federal judge revoked Palij's US citizenship, based on his wartime activities, human rights abuses and postwar immigration fraud.
In this Monday, Aug. 20, 2018, frame from video, Jakiw Palij, a former Nazi concentration camp guard, is carried on a stretcher from his home in the Queens borough of NY.
Palij insisted he and other men in his Polish hometown had been forced to work in the camp, but now stands accused of being complicit in the murders of thousands of Jews.
Republicans on Tuesday swiftly sought to turn the overnight deportation of an alleged Nazi collaborator from USA soil into a rallying cry for Immigration and Customs Enforcement - the agency that physically removed him - and a political cudgel against Democrats who've questioned its mission.
"Palij's removal sends a strong message: The United States will not tolerate those who facilitated Nazi crimes and other human rights violations, and they will not find a safe haven on American soil", the White House said. Trump convinced the Germans to take him, and give him a trial for his crimes.
Berlin officials understood it was a "moral obligation" to accept Palij because he "served in the name of the former German government".
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President Trump, Grenell said, "made it very clear that he wanted this individual out of the U.S".
Grenell said while previous German officials refused to accept Palij, newer members looked at the issues differently, especially Foreign Minister Heiko Maas and Interior Minister Horse Seehofer.
He had been living on welfare in Queens, New York, until his deportation. Protesters have regularly gathered outside of Palij's house and the push for his deportation has garnered bipartisan support.
What made Palij's deportation hard?
Grenell told reporters that there were "difficult conversations" because Palij is not a German citizen and was stateless after losing his US citizenship, but "the moral obligation" of taking in "someone who served in the name of the German government was accepted".
"Good riddance to this war criminal", Senate Majority Leader Chuck Schumer, a New York Democrat, said. "He doesn't deserve to die in the USA, a place of freedom and equality where we respect each other's differences".
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