This is according to prosecutors in the city of Stuttgart.
The deportation took place on Tuesday.
Germar Rudolf, also known as Germar Scheerer, had his emergency petition to block the deportation rejected by the US Supreme Court on Thursday.
Rudolf, a 1989 chemistry graduate of Bonn University and a former student at Max Planck Institute in Stuttgart, Germany, was sentenced in 1995 to 14 months in prison for Holocaust denial, a crime in Germany, but then disappeared.
He had petitioned the US Supreme Court because he was fighting his deportation with the 11th US Circuit Court of Appeals in Atlanta, Georgia, but the next hearing was not scheduled until January - too late to halt the action.
Rudolf's Expert Report on the Formation and Detectability of Cyanide Compounds in the Gas Chambers' of Auschwitz concluded that "no mass gassings with hydrogen cyanide took place in the National Socialist concentration camp Auschwitz".
In sentencing Rudolf, the Stuttgart court cited his "incitement of the people in conjunction with denigration of the memory of the dead, libel and incitement to racial hatred".