The French goalkeeper was knocked out during last weekend's scoreless draw with Everton but returned to the pitch to see out the game.
At the time, Villas-Boas said he felt Lloris was in good enough shape to continue but a week later and he had to sit out after he failed to satisfactorily come through the Immediate Post-Concussion Assessment and Cognitive Testing (ImPACT).
"The medical department felt that it was a bit too soon," Villas-Boas said after Tottenham's 1-0 loss at White Hart Lane.
"Probably had the game been on Monday, he would have played. I expect he will play for France (in the World Cup play-offs).
"For them, it was a bit too soon although clinically and medically all the signs were that the player was ready to play.
"They did a test that they do, that they value a lot, called the ImPACT test, so I had to stick to what they said.
"They decided the player wasn't good enough. That test doesn't serve as an evaluation tool for an assessment, but they thought so and we've gone on from there because we respect them a lot."
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