Liverpool made a move for the Udinese central defender last month, but Villarreal were always at the head of the queue which also included Bayern Munich.
And now, after talks with his agent, Villarreal have come to agreement with the Colombian.
The 24-year-old has agreed a five-year deal and will officially put pen to paper after the Copa America.
"They were the first club to show an interest in him," his agent Jerome Barbadillo said when asked why he opted for Villarreal.
"He is very happy, but is now focused on the Copa America - but he is aware of everything."
The deal is understood to be worth €7milllion and they are also reported to have offered them one of Jozy Altidore or Marco Ruben.