Spurs' 0-0 draw with the Serbian club was marred by the banner that was visible in the home end of the stadium in Belgrade.
UEFA delegates are believed to have taken photographic evidence of the sign ahead of launching an investigation into the incident, which Pochettino labelled as "unacceptable".
"I didn't see it," Pochettino told reporters at full time. "The club is aware but I did not see [it myself].
"But if this is true, then it is an unacceptable thing. It is very disrespectful. This is a shame, very disrespectful and unacceptable."
The Serbian club was previously thrown out of the Europa League in 2007 - then the UEFA Cup - after rioting during a qualifying clash with Zrinjski Mostar.