Loud monkey-chanting was heard to come from the away end on several occasions directed against Jermain Defoe, Aaron Lennon and Andros Townsend in the Group J clash, which ended 0-0 after three Spurs goals were controversially ruled out.
Villas-Boas said he did not hear the chants himself, but he would encourage UEFA, whose head Michel Platini was at the game, to take any action if it is proven that the travelling fans did in fact hurl racist abuse. Villas-Boas said in his post-match press conference: "I think (UEFA will act if the accusations are proven)."
The Portuguese manager added: "UEFA is very active on this kind of situation and our overall objective is to kick racism out of football. I can't point the finger at anyone in any way shape or form because I didn't hear anything. It's for the authorities to follow up in any kind of investigation."
The anti-racism group FARE posted a link on their Twitter feed giving Spurs fans the chance to report any chants they heard from the away end and UEFA have fined clubs in the past for racist incidents.
Tottenham also operate a strict zero-tolerance policy when it comes to racism. Away from the racism furore, Villas-Boas was left to reflect on another disappointing night.
He was happy with his team's performance, but he was far from thrilled with that of referee Ovidiu Alin Hategan. The Romanian ruled out three goals, two of which looked perfectly legal.
In the first half Clint Dempsey's diving header was ruled out for offside even though he looked level and after the interval, Steven Caulker was denied his first Spurs goal for supposedly climbing on Stefano Mauri's back before heading in a cross.
"We managed to put the ball in the net three times but unfortunately because of mistakes from the ref we couldn't get the goals we certainly deserved," said the Portuguese, who also saw a Gareth Bale effort ruled out for offside.
"Mauri is one of the strongest Lazio players in the air and Caulker beat him in the air and scored a legal goal so we don't see anything (wrong). That situation disappoints us."