The Toffees appointed the former Liverpool manager, 61, as Carlo Ancelotti’s successor in June.
Everton, who lost 2-1 to Norwich City on Saturday, have won only one of their last 13 Premier League games and sit 15th in the table, six points above the relegation places.
The club say an update on a permanent replacement will be made in due course.
Everton held an emergency board meeting on Saturday to discuss Benitez’s future following the defeat at Carrow Road, which was a ninth loss in the club’s past 12 league games.
Everton’s travelling contingent demanded Benitez “get out of our club”, while another supporter invaded the pitch in an attempt to confront the Spaniard.
Benitez, whose previous job in the Premier League was at Newcastle United, leaves Everton with a win percentage of 31.8% – his lowest record in charge of an English club.
|Rafael Benitez as manager of English clubs|
|Club (years)||Games managed||Games won||Win %|