Confirmation the Argentine had stood down as boss of La Roja came five days after the federation announced that talks over his future had broken down.
Sampaoli leaves after a week of acrimony in which he claimed the federation was holding him hostage over a $6 million (5.5 million euros) buy out clause in his contract which still had two years to run.
Chile coach Sampaoli set to quit
He had also been angered by local media reports linking him to tax evasion and holding an offshore bank account.
The federation confirmed his departure in a statement.
"A deal has been reached between the national professional football association and Jorge Sampaoli to bring to an end their contractual relationship," it said.
Contenders to succeed him include his compatriot Marcelo Bielsa, jobless since walking out on Marseille at the start of the Ligue 1 season in France, could return to the post he held between 2007-2010.
Another name reportedly in the frame is Eduardo Berizzo, the manager of Celta Vigo in Spain's La Liga.
Aside from qualification for the 2018 World Cup, Chile are also preparing to defend their title at the Copa Centenario in the United States later this year.
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