Demjanjuk, 89, arrived in an ambulance at Cleveland Burke Lakefront Airport after spending several hours with U.S. immigration officials at a downtown federal building.
The plane arrived in Germany Tuesday morning.
He was to be brought before a judge and formally arrested. He also has to undergo a medical evaluation to see if he is fit to stand trial.
The deportation came four days after the U.S. Supreme Court refused to consider Demjanjuk's request to block deportation and about 3 1/2 years after he was last ordered deported.
The Ukrainian-born Demjanjuk is wanted on a Munich arrest warrant that accuses him of 29,000 counts of accessory to murder as a guard at the Sobibor death camp in Nazi-occupied Poland. The legal case spans three decades.
Demjanjuk denies Germany's accusations, saying he was held by the Germans as a Soviet prisoner of war and was never a camp guard. Demjanjuk's family fought deportation, arguing he is in poor health and might not survive the trans-Atlantic journey.
Rabbi Marvin Hier, a founder of the Los Angeles-based Simon Wiesenthal Center, has no sympathy for the elderly defendant.
"When people say 'Well, he's 89 years old,' I do not have any compassion for that. He lived a full life. He avoided the bar of justice. He watched his family celebrate birthdays and occasions - something that was denied to all of his victims." Hier told CBS News.
Hier also said this will probably be the last trial of someone accused of Nazi war crimes.
"In order to have a trial you have to have personal testimony of the victims and all of them are now in their 80s … and eventually this will come to a biological end," he said.
The center was established to locate and help bring to justice Nazi war criminals.
The deportation capped a day in which Demjanjuk said goodbye to his family and was visited by two priests at his home in a Cleveland suburb.
He then slipped quietly into an ambulance parked in his driveway, his family members standing at the edge of the garage and holding up a floral-patterned bedsheet to block the view of reporters and photographers across the street.
Earlier Monday, his son, John Demjanjuk Jr., said an appeal in a U.S. court would go ahead even if his father isn't in the country.
"Given the history of this case and not a shred of evidence that he ever hurt one person let alone murdered anyone anywhere, this is inhuman even if the courts have said it is lawful," Demjanjuk Jr. said.
Also Monday, a Berlin court rejected an appeal aimed at preventing deportation.
Once in Germany, Demjanjuk will be brought before a judge and formally charged. He will also be given the opportunity to make a statement to the court, in keeping with standard procedure, Staudigl said.
Demjanjuk is expected to be held in the medical unit of a Munich prison. The government has said preparations have been made at the facility to ensure he will receive appropriate care.
The case dates to 1977 when the Justice Department moved to revoke Demjanjuk's U.S. citizenship, alleging he hid his past as a Nazi death camp guard.
Demjanjuk had been tried in Israel after accusations surfaced that he was the notorious "Ivan the Terrible" at the Treblinka death camp in Poland. He was found guilty in 1988 of war crimes and crimes against humanity, a conviction overturned by the Israeli Supreme Court.
A U.S. judge revoked his citizenship in 2002 based on U.S. Justice Department evidence showing he concealed his service at Sobibor and other Nazi-run death and forced-labor camps.
An immigration judge ruled in 2005 he could be deported to Germany, Poland or Ukraine. Munich prosecutors issued an arrest warrant for him in March.