The court noted that Premier League club Beitar had been found guilty of offenses involving racist abuse for the fourth time this season, far more than any other Israeli club.
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The incident cited in the referee's report that led to the charge involved a section of Beitar's supporters shouting racial abuse at Hapoel Kiryat Shmona's Ahmed Abed, who scored a late winner for the visitors in a league match at the weekend.
"There is no other example of a club repeatedly facing a charge of this kind... and justice must be meted out," the court said in its ruling.
Beitar's representatives said they were acting to try to stamp out racism among the fans but the court said it could not ignore the fact that these efforts had failed and severe punishment was mandatory.
Beitar are the only Israeli club never to have employed an Arab player and their supporters regularly chant racist abuse for which they have repeatedly faced disciplinary action.
All other top Israeli clubs regularly field Arab players and since the 1970s Arabs have played in Israel's national team.
The point deduction pushed Beitar down a place to fifth behind Maccabi Haifa on goal difference with 43 points from 32 matches. The top four qualify for European competition.