At a brief hearing in Adelaide Magistrates' Court, chief magistrate Kelvyn Prescott ordered Bradley John Murdoch, 45, to appear in court in the northern port city of Darwin tomorrow in relation to the murder in 2001.
The body of Mr Falconio, 28, of Hepworth, has never been found.
Murdoch was expected to be flown to the Northern Territory under tight police guard.
Handcuffed and flanked by prison officers and court staff, Murdoch showed no expression in court early today as Mr Prescott issued the order.
Murdoch's lawyer Grant Algie argued the arrest on Monday was illegal because it occurred while Murdoch was being detained in basement cells in the Adelaide's District Court, where he was earlier acquitted of unrelated sex offences involving a 12-year-old girl and her mother.
The magistrate dismissed the argument.
Police in Darwin issued an arrest warrant for Murdoch after DNA tests linked him to the suspected killing of Mr Falconio.
He is believed to have been killed after he and girlfriend Joanne Lees, of Almondbury, who now lives and works in Brighton, were flagged down by a gunman as they drove along the Stuart Highway in central Australia on the night of July 14, 2001.
Miss Lees managed to escape and raise the alarm, sparking one of the biggest manhunts in Australian history.
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