Emmanuel Adebayor scored a crucial away goal to knock out Inter as Spurs reached the Europa League last eight.
"It was very, very easy to hear the chanting so I am sure that Uefa will act on it," said Villas-Boas.
"It's difficult for Inter because it is something that has happened before."
Tottenham lost the game 4-1 on the night, but Adebayor's goal in extra time meant the tie finished 4-4 on aggregate with Spurs winning on away goals.
Villas-Boas, a former coach at Inter under Jose Mourinho, added: "It doesn't mar the game but it is something that should have been avoided."
Inter have already been fined £43,000 (50,000 euros) by Serie A officials this season after their fans were found guilty of racially abusing former Inter players Mario Balotelli and Sulley Muntari, who now play for AC Milan, in the Milan derby last month.
England: Chelsea, Newcastle United, Tottenham Hotspur
Italy: Lazio
Portugal: Benfica
Russia: Rubin Kazan
Switzerland: FC Basel
Turkey: Fenerbahce
Quarter-final draw to be made on Friday.
Uefa has also fined Lazio on two separate occasions this season for their fans' behaviour, including racist chanting, during Europa League group matches against Spurs.During Inter's win over Tottenham, monkey chants were reported with an inflatable banana also seen in the crowd.
Adebayor's 96th-minute extra-time goal came after Inter had dragged themselves back from a three-goal deficit in the first leg at White Hart Lane.
Antonio Cassano's first-half header was followed up by Rodrigo Palacio's strike and a William Gallas own-goal, but Adebayor's finish meant that Inter needed another two goals to progress, despite pulling one back through Ricardo Alvarez.
The result was Tottenham's first defeat in the Europa League this season, but they join Chelsea and Newcastle in the competition's quarter-finals.
Villas-Boas, who steered Porto to Europa League success in 2011, added: "The players have been magnificent to get us into the quarter finals.
"It's a valuable lesson for us tonight, but we have players who can make a difference in the important moments. We are happy to go through. The players kept fighting in extra time, showing they wanted it and we look forward to the draw."
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