According to reports in French media, Benatia confronted match officials during halftime in Marseille's 3-2 win over Olympique Lyonnais on September 22nd to complain about a red card shown to Leonardo Balerdi in the fifth minute.
On Wednesday, the French football league's governing body (LFP) said Benatia would receive a "three-match suspension and three-match suspended suspension from the bench, referees' locker room and all official functions."
In a statement on Wednesday, Marseille said they had taken note of the decision.
"The club profoundly disagrees with this decision and considers the treatment meted out to its sporting advisor to be totally disproportionate, despite the fact that he was neither guilty of insulting nor threatening the referees," Marseille added.
"This decision is all the more surprising and incomprehensible in that it is neither coherent nor balanced with regard to similar situations or events that have occurred recently or in the more distant past, and on which the committee has ruled."
Marseille, who are third in the standings, host bottom side Angers on Friday.
