The 46-year-old Spaniard has reached "an agreement in principle" to take over the Russian top-flight team, the club said on their Twitter account on Thursday.
Gracia has also previously worked at Spanish sides Almeria and Osasuna.
Rubin finished 10th in the league this season under Valery Chaly who has not been offered a new contract.
(Reporting by Dmitriy Rogovitskiy; Editing by Tony Jimenez)
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