Kondogbia, linked with Arsenal and Real Madrid this summer, has a buy-out worth £17.2million - which has now been met.
Kondogbia is partly owned by Doyen Sports Investments - the same company who have a stake in Radamel Falcao - and now the Frenchman is believed to be on his way with the Colombian to Monaco.
Sevilla confirmed in a statement: "Geoffrey Kondogbia is already history at Sevilla FC. The French international has officially informed the club that he will unilaterally rescind his contract."
Jose Maria del Nido admits he does not hold anything against the player or Monaco.
"Since last week, we have heard that this was going to happen," revealed Del Nido to the local media.
"We considered the possibility and from there we have brought in [Stephane] Mbia, who ultimately comes in to cover the position but who can also play at centre-back.
"Monaco have known that Sevilla had closed its doors. We have referred them to the buyout clause and they have acted as such against the will of Sevilla.
"I would think that there has been no lack of professionalism and I understand that he has been professional.
"The image he presented at Levante [at the weekend] was not that of something on their way out."
Kondogbia is just the latest departure from Sevilla following on from Gary Medel, Jesus Navas, Alvaro Negredo, Antonio Luna, Luis Alberto and Jose Campana this summer - but Del Nido insists the club has planned for it.
"Events have allowed us to accelerate plans of change that we had established for the medium term," he said.
"The market has indicated that economically at least our team was good, because if it wasn't, the players would have stayed and we would not have brought in more than €100m."