Spurs boss Andre Villas-Boas claimed the 26-year-old goalkeeper looked "ready to play" a week on from being knocked unconscious during the draw at Everton, but the medical advice suggested otherwise.
Villas-Boas revealed that the France international 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 Lloris being unavailable, Villas-Boas said he stands by his previous stance and rejected the notion that his absence against Newcastle 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."