The man was charged with three offences including possession of the material and importing the doll, which carries a maximum penalty of 10 years behind bars and 2500 penalty units, equating to a fine of $525,000.
For the possession of the "anatomically correct" doll alone, if convicted he faces a potential jail term of up to 15 years.
The charge was introduced in September 2019.
According to the AFP, it includes possession of an "object that resembles a child or part of a child under 18, and a reasonable person would consider it likely that the doll is intended to be used to simulate sexual intercourse".
Home Affairs Minister Peter Dutton said the laws were passed to "ensure the safety of our children is always put first".
"We passed these tough laws last year to better equip our law enforcement agencies to stamp out these insidious crimes," Mr Dutton said in a statement to news.com.au.
"This arrest is another example of our federal and state agencies working closely together and I pay tribute to the hardworking officers who dedicate themselves to making our communities a safer place."
AFP Acting Commander South Australia Gail McClure said the dolls objectified children as sexual beings and could desensitise anyone who used them to the physical, emotional and psychological harm caused by sexual abuse.
"Some dolls are even robotic and designed to respond positively to the abuse," she said.
The man, from the state's southeast, was granted bail and is expected to face Naracoorte Magistrates Court on March 27.
All importations of childlike sex dolls are seized if they are intercepted by AFP officers.