The Spanish outfit triggered their option to permanently sign the French defender after parting with a reported €25m to secure the 25-year-old on a four-year deal until 2022.
The club have revealed an €80m release clause has been included in Kondogbia's contract following an impressive season that saw the midfielder play an instrumental role in Valencia's stunning 4th placed La Liga finish.
Kondogbia featured in 31 league games, scoring four goals and providing four assists, where his power, pace, technique and game intelligence saw him stamp his mark in the competition after overcoming a relatively disastrous period with former club Inter.
Following an impressive campaign, Kondogbia emerged as a summer target for a host of European clubs, including Premier League side Tottenham who remain on the lookout for a long-term replacement for Mousa Dembele.
In four of his last five seasons, Kondogbia has played for four different sides in three different leagues having featured for Sevilla, Monaco, Inter and Valencia since season 2013/14.
However, despite an exceptional season the 25-year-old failed to be named in Didier Deschamps' France squad for this summer's World Cup in Russia.