The former Valencia winger will move to Italy once the formalities of the transfer are completed, having enjoyed a career renaissance over two years in southern Spain
The 31-year-old has agreed terms in principal with la Viola and is set to join Vincenzo Montella's side once personal terms and a medical have been fully completed.
"Fiorentina and Malaga announce they have reached an agreement for the permanent transfer of Joaquin Sanchez Rodriguez," read a statement on Fiorentina's official website.
The experienced midfielder made 45 appearances last season for Malaga in all competitions, including 10 in the club's run to the Champions League quarter-finals, where they suffered an agonising 3-2 defeat to Borussia Dortmund.
Joaquin, who played for Betis and Valencia prior to his move to los Boquerones, has also won 51 senior caps for Spain.