Facundo Jones Huala, the leader of the militant Mapuche group RAM, was extradited to Chile on Tuesday afternoon.
The Mapuche leader is wanted in Chile on a number of charges including the destruction of private property and the illegal possession of firearms. If found guilty there, he could spend up to 10 years in jail.
Jones Huala was taken by helicopter from the southern city of Esquel, where he has been jailed since June 2017, to Mendoza for transfer to Santiago, Noticias Argentinas reported.
The United Nations last week requested the suspension of the extradition. For its part, Argentina's Supreme Court in late August voted against a request by Jones Huala's legal team to block the measure.
In March, federal judge Gustavo Villanueva's decision to accept Chile's extradition request prompted an outbreak of violence in the southern city of Bariloche, where protesters threw rocks at Border Patrol and Airport Security Police. Fifteen people were detained including eight men, seven women and a 14-year-old.
Jones Huala's name gained further prominence late last year amid the disappearance and death of 28-year-old artisan Santiago Maldonado.
Supporters of the Mapuche movement say the Mauricio Macri government is criminalising outspoken indigenous communities to create "an internal enemy" that can justify its security and police reform agenda.