The flag was an imitation of the logo from BBC comedy show Only Fools and Horses, with some words modified to form an offensive slogan.
Spurs manager Mauricio Pochettino described the banner as "very disrespectful and unacceptable".
The clubs drew 0-0 in Thursday's Europa League match at the Partizan Stadium.
Tottenham officials made Uefa aware of the banner before the break and delegates took photographic evidence after the match.
"The club is aware but I did not see it," said Pochettino. "If this is true, then it is an unacceptable thing,"
Spurs have a historical association with London's Jewish community.
In 2007, Partizan were thrown out of the Uefa Cup and fined for rioting during a first qualifying round first-leg clash at Zrinjski Mostar.