Narumi Kurosaki, then 21, vanished from her university after eating with Nicolas Zepeda, who returned to Chile by the time her disappearance was reported days later.
French investigators believe Kurosaki was killed by Zepeda in a jealous rage but her body was never found despite extensive searches.
Last month, Chile agreed to extradite Zepeda, 29.
On Monday, the country's top court "confirmed the judgement delivered on April 2," according to the decision seen by AFP.
Kurosaki was living on a university campus in Besancon, France on December 4, 2016 when she was last seen alive.
Her body has never been found.
"I'm delighted with this decision," Besancon's public prosecutor Etienne Manteaux told AFP.
"This extradition will allow for a trial with the presence of the suspect, who will be able to defend himself."
Manteaux also praised Chilean authorities for agreeing to the extradition despite the absence of a treaty between the two countries.
According to investigators, Zepeda went to Besancon at the beginning of December 2016 to see his former girlfriend.
On the evening of December 4, the pair entered her residence together.
The prosecutor said several students heard "howls of terror, cries" that night but no-one called the police.
Kurosaki's disappearance was not reported for several days.
Zepeda, the son of a wealthy Chilean family, met Kurosaki in Japan in 2014.
At the time of her disappearance, the pair had broken up and she was in a new relationship.