On Thursday the court in Lliria, near Valencia, also charged the former Portugal Under-21 player with robbery, assault, "illegal detention" and possession of illegal weapons.
Semedo denies the allegations.
Semedo, 23, has played five times since joining Villarreal for £12m (14m euros) from Sporting Lisbon in the summer.
A club statement read: "While always respecting the notion that everyone is innocent until proven guilty, the club has decided to suspend the player from duties without pay until the ongoing case has been settled.
"Villarreal would like to show its horror at the grave crimes the player Ruben Semedo was charged with." AGENCIES