The Ligue 1 side reportedly triggered the 20-year-old's €20m (£17.2m) release clause earlier this week, and the Spanish team have revealed that the Frenchman's contract with the club will now be terminated.
"French midfielder Geoffrey Kondogbia is history at Sevilla FC," read a statement from the club.
"The club will terminate his contract after his termination clause was invoked. The €20m collected will be deposited with the Football League shortly.
"He was absent from training this afternoon and has failed to speak with his teammates."
The once-capped French international arrived at the Ramon Sanchez Pizjuan last summer.