Calleja, who played for Villarreal from 1999-2006, has coached at the club for six years at youth level, taking over Villarreal B at the start of this season.
“Villarreal and Javi Calleja have reached a deal which sees him become the first-team coach of the ‘Yellow’ side for the 2017-18 season,” the club said in a statement.
Escriba was dismissed with Villarreal 14th in the La Liga standings after six games in which they suffered three defeats, including a humiliating 4-0 beating by promoted Getafe on Sunday.
The former Getafe coach had renewed his contract in May to the end of this season after being appointed in August 2016.
Villarreal were promoted to Spain’s top flight in 1998 and 10 years later finished runners-up to Real Madrid in their best league campaign.
The team nicknamed “Yellow Submarine” suffered a shock relegation in 2012 but were immediately promoted the following year and have played in the Europa League each season since.