A spokesman for the prosecutor's office in the southern city of Nuremberg told AFP that the warrant pertained to the murder of German student Rolf Stawowiok in the 1970s.
"The prosecutor's office applied for an arrest warrant at the end of December and it has come through in the meantime," he said.
Videla, now 84, is currently serving a life term at an Argentine barracks on multiple charges of human rights violations while he was at the helm of the country's military junta from 1976 to 1981.
The Nuremberg prosecutor's office opened a probe into the junta's former leaders including Videla at the end of the 1990s over the killing and disappearance of Germans during the so-called Dirty War. But it dropped the cases after Argentine authorities rejected an extradition request.
German authorities reopened the case last year when Stawowiok's remains were discovered in Argentina showing that he had been shot several times. During the years of junta rule some 30,000 people vanished and are still unaccounted for.
Videla was sentenced to life in prison for his crimes in 1985 but was pardoned and released in 1990 under former President Carlos Menem, only to be arrested again in 1998 for kidnapping children and other charges not included in his pardons.