It activated a suspended two-point punishment the club had received last year in place of a point that was deducted for a similar offence but was reinstated on appeal.
In its ruling the court said "the Beitar management had not made an honest effort to combat the fans' chants and was resigned to accepting them."
Beitar have the worst disciplinary record in Israel's
Premier League. Since 2005 they have faced more than 20 hearings and have received various punishments, including points deductions, fines and matches behind closed doors.
The outfit is a bastion of Israel's political right-wing and the only leading club in the Jewish state that has never signed an Arab player because of fan pressure.
Beitar were Israel's richest club until four seasons ago when their main financial backer, Russian-born billionaire Arcadi Gaydamak, stopped most of his funding, although he continues to own the club.
Beitar are 14th in the 16-team Premier League and the deduction leaves them with 15 points from 19 matches, level on points with 15th-placed Ironi Rishon Lezion. Three clubs are due to be relegated at the end of the season.