The Portuguese claimed the 26-year-old goalkeeper looked "ready to play" a week on from being knocked unconscious and in need of lengthy treatment on the pitch after a collision with Everton forward Romelu Lukaku last Sunday, but the medical advice suggested otherwise.
FIFA's medical chief was among those to question the decision not to substitute Lloris at Goodison Park, yet the club's medical staff said they were "totally satisfied that he was fit to continue playing" in that match.
The France captain was rested for Thursday's Europa League win over Sheriff Tiraspol after the blow, but Villas-Boas claimed after that tie that Lloris would return against Newcastle.
However, Brad Friedel once again deputised in the 1-0 defeat after which Villas-Boas revealed Lloris failed to satisfactorily come through Immediate Post-Concussion Assessment and Cognitive Testing (ImPACT) - a computerised concussion evaluation system.
"The medical department felt that it was a bit too soon," the Portuguese said.
"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."
Despite the fact Lloris was again unavailable, Villas-Boas stands by his previous stance and rejected the notion that his absence on Sunday indicated he had been wrong to leave him on against Everton.
"No, not in my opinion, sorry," he said.
"Nothing has come to light, the player is absolutely fine.
"The tests that they have, you don't know because they have made different tests.
"I think, if obviously the club agree, it would be welcome for the medical department to speak up their voice about the situation.
"The only thing that I can tell you and the only comment that I am going to make is that the medical department advised not to use the player. We followed rules and that's it."
Villas-Boas reiterated that it was "extremely important" to put forward a member of the medical department to clarify matters of the last seven days, perhaps unaware of a statement shortly before the Newcastle match from Wayne Diesel, head of medical services, explaining the absence.
"We've continued to monitor Hugo all week and after discussions, Andre and the medical department have agreed to afford the player a couple more days' rest," he said.
"Hugo is naturally disappointed as he was keen to return to action however we feel this decision is in the player's best interest."
Spurs had earlier been accused by a former United States international of endangering the life of Lloris after allowing him to continue against Everton.
The career of Taylor Twellman was ended after he was concussed a seventh time and the 33-year-old, who now campaigns to raise awareness over the damage caused by brain injuries in sport, is staggered by the actions of Tottenham and Villas-Boas.
Twellman insists Spurs ''played with Lloris' life'' by putting him at risk of incurring 'second impact syndrome' - a second successive concussion that can lead to death or severe disability.
''It was ridiculous, but I'm actually grateful for what Tottenham did because it is 100 per cent not the way to handle a concussion,'' Twellman told Radio 5 Live's Sportsweek programme on Sunday morning.
''We're not talking about a career here, they played with Lloris' life.''
Villas-Boas said on Wednesday that those who criticised the club's actions over Lloris were ''incompetent people'' but Twellman added: ''Anyone who tells me I'm uninformed or if AVB wants to tell me I'm incompetent, I'm not. Science has shown us there's no test that can show concussion."