The Spaniard was seen hurling a bottle that struck referee Clos Gomez in the face after the final whistle in the Primera Division encounter with Real Madrid last weekend
A late David Cortes own goal gifted champions Real Madrid a 2-1 victory, with both Moises Hurtado and Guilherme Siqueira sent off for their angry protests after the final whistle.
Referee Clos Gomez was then hit in the face by a bottle thrown by Dani Benitez, who later apologised for his actions in the post-match press conference.
But the 25-year-old, who is on loan from Udinese, has now been hit with a three-month ban coming into effect immediately, meaning he will not available for the crucial clash with Rayo Vallecano on Sunday.
The punishment must be served within competition period, so Benitez will be barred from match action until mid-November, effectively missing up to 15 games for the club.
Granada sit just two points above the relegation places at 15th in the Primera Division standings and need to avoid defeat in their final league clash with Rayo to secure their top-flight status.