Assistant referee David Bryan was struck by a flare thrown from the Spurs end in the first half with the issue now to be investigated by the FA.
After the match, in which Andros Townsend and Roberto Soldado scored, Villas-Boas said: "It is not great to see.
"It should be avoided completely. It touched the linesman and situations like this don't have a place in football. I sincerely hope it doesn't happen again."
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