An extra-time goal from the Togo strike ensured the north London club progressed to the Europa League quarter-finals on away goals, yet their overall success has been overshadowed by the incident.
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Speaking after the game, Villas-Boas said: "Chants were very, very easy to hear.
"It's difficult for Inter, we have seen it before. It doesn't mar the game but it is something to be avoided."
Lazio were fined £120,000 by Uefa after their fans racially abused Spurs players in their meeting at the Stadio Olimpico in the Europa League group stage back in November.
The club they were also punished for similar behaviour in the meeting at White Hart Lane earlier in the season.