Having already removed director of football Victor Orta, the club announced the departure of Spaniard Gracia on Wednesday along with his backroom staff.
Gracia, who only arrived at Leeds in February, leaves the club after four defeats in five Premier League games — they are outside the drop zone on goal difference with four games remaining.
“Leeds can confirm Javi Gracia will leave the club after 12 games in charge,” a club statement said. “Zigor Aranalde, Mikel Antia and Juan Solla, who joined alongside Gracia, will also leave the club.
“We thank Javi and his team for their efforts under difficult circumstances.
“The remaining four games of the season will be overseen by experienced head coach Sam Allardyce.”
Allardyce suffered his first Premier League relegation when West Brom went down in 2021, leaving the club six months into an 18-month contract.
The 68-year-old former Bolton, Newcastle, West Ham and England boss becomes Leeds’ third permanent manager of the season after Jesse Marsch and Gracia.