Valverde is said to have waited for Baena in the car park of the Santiago Bernabeu and attacked him after Villarreal beat Real Madrid 2-1 on Saturday.
Villarreal confirmed that the Baena has made a complaint to the police.
"Villarreal CF player Alex Baena was assaulted last night while on his way to the team bus after the match against Real Madrid CF at the Santiago Bernabeu stadium," a statement on the club's website read.
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"Faced with this situation, the player has decided to file a complaint against the aggressor with the police. Once again, Villarreal CF rejects any act of violence and firmly believes in the player’s version of events and will support him throughout this process."
More to follow...