Former AC Milan coach Fonseca paid a heavy price after seeing red during his side’s 2-1 win over Brest in Ligue 1 on Sunday.
Fonseca only replaced the sacked Pierre Sage at the former multiple French champions four weeks ago.
Now he finds himself in the complicated position of being banned from the dugout and referee’s changing room until November 30.
The commission’s president, Sebastien Deneux, announced that Fonseca has also been banned from entering his team’s changing rooms until mid-September.
Deneux said Fonseca had displayed an intimidating and threatening attitude by throwing himself at the referee and shouting at him.
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Since the Portuguese’s arrival on January 31, he has overseen only three games, an opening defeat to Marseille, a 4-0 win over Reims, and Sunday’s defeat of Brest to leave Lyon in sixth place.
The ruling falls a week after Marseille president, Pablo Longoria, was banned for 15 matches for accusations of refereeing corruption in the aftermath of his side’s 3-0 loss at Auxerre.
Deneux further said the commission regrets that a major figure in Ligue 1 has again demonstrated such behaviour, adding that Fonseca, a coach in Ligue 1, is above all a teacher and his attitude is completely incompatible with his duties.