A much-changed Spurs side got their Group C campaign off to a sturdy start by securing a hard-fought, 0-0 draw in an intimidating atmosphere in the Serbian capital.
It was a solid performance overshadowed by an anti-Semitic banner in the home end, inspired by the Only Fools and Horses logo.
The name was changed to 'Only Jews and Pussies' and was displayed at Partizan Stadium throughout the match.
UEFA is investigating the issue pointed out to them by Tottenham officials, with a delegate from the governing body taking photographic evidence after the match.
"I didn't see it," Spurs boss Pochettino said
"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."
It is not the first time Partizan have found themselves in hot water, having been thrown out of the UEFA Cup and fined in 2007 for rioting during a first qualifying round first-leg clash at Zrinjski Mostar.
Thursday's incident also came just two years on from the disgusting racial abuse suffered by England Under-21s in a European Championship play-off in Serbia.
Spurs left-back Danny Rose was caught up in the problems that night and was among those rested for the clash with Partizan.
Emmanuel Adebayor, Younes Kaboul, Mousa Dembele and Nacer Chadli also remained in north London as Pochettino made sweeping changes.
It was perhaps unsurprising, therefore, to see Spurs struggle for attacking coherence in Serbia, where they had to defend resolutely on a night in which Benjamin Stambouli and Federico Fazio impressed on their full debuts.
"I am happy with the performance [of Fazio]," Pochettino said
"It was his first game, like Stambouli.
"They played first time with us and it is always difficult to make your debut, but I am happy.
"I think the result was fair because I think that Partizan in the second half played well and we did well in the first half
In the end, it is a fair result."
A dead leg sustained by Andros Townsend was the only on-field issue Spurs had in Serbia, meaning they return to Barclays Premier League action against West Brom on Sunday fresh from a solid start to Group C.
"We had a lot of positive things," Pochettino added.
"It is true before the game we wanted three points, but when you analyse the game the result is fair.
"We need to take a lot of positive things and move forward."
As for Partizan counterpart Marko Nikolic, he was filled with pride in the way his side frustrated Spurs.
The head coach, though, was clearly unaware of the issue surrounding the anti-Semitic banner when he thanked the crowd for their behaviour.
"I want to congratulate the crowd," Nikolic said
"The support was great and not only great but everything went well.
"It was a wonderful, sporting environment without the slightest problem."
Source: PA