Tottenham progressed on away goals after losing 4-1 against Inter, but the game was tarnished by the actions of the home support as monkey chants were heard at the San Siro and an inflatable banana was seen in the crowd.
Emmanuel Adebayor, who scored the crucial goal in extra-time, appeared to be the target of much of the racist abuse and Spurs manager Villas-Boas believes UEFA will take action.
"It's a very sensitive situation," Villas-Boas said of the chanting. "UEFA set out to act on that situation.
"It was very, very easy to hear the chanting so I am sure that UEFA will act on it.
"It's difficult for Inter Milan because it is something that in some way has happened before.
"It doesn't mar the game but it is something that should have been avoided."
The fact Tottenham had to contend with racist abuse understandably overshadowed what was a difficult night on the field.
Having romped to a 3-0 win the first leg, Spurs were outclassed at the San Siro as Antonio Cassano, Rodrigo Palacio and a William Gallas own goal took the game to extra-time.
Inter scored again through Ricardo Alvarez but not until after Adebayor scored the vital away goal.
Villas-Boas said: "We set out today to try and get a goal away that would put us in an extremely confident position.
"I think today what happened to us was a bit like what happened to Inter in London.
"They are not as bad as their performance in London and we're not as a bad as the performance we showed today.
"There are still lots of positives in an evening like this because the desire to reach the last eight of the competition was always there from the players, even in extra-time, which is an excellent sign for us."