The Yellow Submarine announced last week that Quique Setien had been sacked as manager following a disappointing start to the 2023-24 campaign.
Raul was strongly linked with a move to Villarreal, with a recent report claiming that the legendary Real Madrid forward, who is in charge of Real Madrid Castilla, had held talks over a move to Estadio de la Ceramica.
However, it has now been confirmed that Pacheta has been appointed as the new boss for the rest of the season.
"Villarreal CF and the coach from Burgos have reached an agreement for the rest of the season," read a statement on the Spanish club's official website.
"Villarreal CF and Jose Rojo Martín 'Pacheta' have reached an agreement for the manager from Burgos to become the Submarine's head coach for the rest of this season.
"Alongside Pacheta, Chema Monzon (assistant head coach), Jorge Trigueros (fitness coach) and Guille Galmes (analyst) have all joined the club."
The 55-year-old last managed Real Valladolid between 2021 and 2023, while he has also been in charge of the likes of Oviedo, Hercules, Elche and Huesca.
Pacheta was dismissed as Real Valladolid head coach in April due to a poor run of form, but he has now returned to Spain's top flight with Villarreal.
Raul will therefore remain head coach of Real Madrid Castilla, which is a position that he has held since 2019.
Real Madrid first-team manager Carlo Ancelotti only has a contract at Bernabeu until next June, and it is understood that Raul is in contention for the head coach position with the capital giants.
Villarreal finished fifth in La Liga last season, but a disappointing start to the 2023-24 campaign has left them down in 15th position in the table on three points from four matches.
The Yellow Submarine suffered a 4-3 home defeat to Barcelona at the end of August before entering the international break off the back of a 3-1 loss at Cadiz.
Pacheta's first match in charge of Villarreal will come against Almeria on September 17.