Quesada takes over from Mario Ledesma, who left to replace Daniel Hourcade as Argentina boss last week.
Capped 38 times by the Pumas, Quesada has left his role at Biarritz to return to his homeland with the Jaguares, who reached the Super Rugby play-offs under Ledesma this year.
"It was time to go back to my country and bring Argentine rugby all my experience," said Quesada, who guided Stade Francais to the Top 14 title in 2015 and the European Challenge Cup two years later.
— JaguaresARG (@JaguaresARG) August 8, 2018
"There is an emotional part of this decision to join the Jaguares. It is a great adventure that I want to experience in depth and I really want to go through.
"You have to take the good things done by Aspirina Perez and then Mario Ledesma, to work and look for the Jaguares to continue growing."
Photo Getty Images. Caption: New Jaguares coach Gonzalo Quesada